Starting phenix.real_space_refine on Thu Jul 2 13:31:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22xc_68747/07_2026/22xc_68747.cif Found real_map, /net/cci-nas-00/data/ceres_data/22xc_68747/07_2026/22xc_68747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/22xc_68747/07_2026/22xc_68747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22xc_68747/07_2026/22xc_68747.map" model { file = "/net/cci-nas-00/data/ceres_data/22xc_68747/07_2026/22xc_68747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22xc_68747/07_2026/22xc_68747.cif" } resolution = 3.28 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= 0.018 sd= 0.018 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 P 3 5.49 5 S 45 5.16 5 C 5790 2.51 5 N 1337 2.21 5 O 1448 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8623 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 586 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "B" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 586 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "C" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2218 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 263} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 586 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "G" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2218 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 263} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 2207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2207 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 262} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'CLR': 1, 'D21': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'CLR': 1, 'D21': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'CLR': 1, 'D21': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.65, per 1000 atoms: 0.19 Number of scatterers: 8623 At special positions: 0 Unit cell: (101.76, 100.818, 86.6842, 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 45 16.00 P 3 15.00 O 1448 8.00 N 1337 7.00 C 5790 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 28 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 109 " - pdb=" SG CYS C 186 " distance=2.03 Simple disulfide: pdb=" SG CYS G 28 " - pdb=" SG CYS G 274 " distance=2.03 Simple disulfide: pdb=" SG CYS G 109 " - pdb=" SG CYS G 186 " distance=2.03 Simple disulfide: pdb=" SG CYS R 28 " - pdb=" SG CYS R 274 " distance=2.03 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 186 " distance=2.03 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: 0.60 Conformation dependent library (CDL) restraints added in 325.1 milliseconds 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1972 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 7 sheets defined 78.2% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 9 through 32 removed outlier: 6.825A pdb=" N GLU A 22 " --> pdb=" O LYS A 18 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLU A 23 " --> pdb=" O GLU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 73 removed outlier: 3.875A pdb=" N ARG A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 32 removed outlier: 6.787A pdb=" N GLU B 22 " --> pdb=" O LYS B 18 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N GLU B 23 " --> pdb=" O GLU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 73 removed outlier: 3.947A pdb=" N ARG B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 64 removed outlier: 3.758A pdb=" N ILE C 39 " --> pdb=" O ASN C 35 " (cutoff:3.500A) Proline residue: C 42 - end of helix Processing helix chain 'C' and resid 72 through 90 removed outlier: 4.048A pdb=" N TYR C 76 " --> pdb=" O MET C 72 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 100 removed outlier: 3.554A pdb=" N TRP C 94 " --> pdb=" O THR C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 139 removed outlier: 4.004A pdb=" N LEU C 120 " --> pdb=" O TYR C 116 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR C 121 " --> pdb=" O THR C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 154 removed outlier: 3.511A pdb=" N LYS C 149 " --> pdb=" O GLN C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 167 removed outlier: 4.149A pdb=" N VAL C 158 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE C 162 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Proline residue: C 163 - end of helix Processing helix chain 'C' and resid 168 through 174 Processing helix chain 'C' and resid 192 through 227 removed outlier: 3.776A pdb=" N VAL C 196 " --> pdb=" O ASN C 192 " (cutoff:3.500A) Proline residue: C 211 - end of helix removed outlier: 3.769A pdb=" N SER C 227 " --> pdb=" O ILE C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 267 Proline residue: C 254 - end of helix Processing helix chain 'C' and resid 274 through 291 Processing helix chain 'C' and resid 293 through 305 removed outlier: 3.976A pdb=" N ASN C 298 " --> pdb=" O HIS C 294 " (cutoff:3.500A) Proline residue: C 299 - end of helix removed outlier: 3.544A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 32 removed outlier: 6.858A pdb=" N GLU D 22 " --> pdb=" O LYS D 18 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N GLU D 23 " --> pdb=" O GLU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 73 removed outlier: 3.955A pdb=" N ARG D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 64 removed outlier: 3.780A pdb=" N ILE G 39 " --> pdb=" O ASN G 35 " (cutoff:3.500A) Proline residue: G 42 - end of helix Processing helix chain 'G' and resid 72 through 89 removed outlier: 4.081A pdb=" N TYR G 76 " --> pdb=" O MET G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 100 removed outlier: 3.562A pdb=" N TRP G 94 " --> pdb=" O THR G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 139 removed outlier: 3.523A pdb=" N LYS G 110 " --> pdb=" O ASN G 106 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR G 121 " --> pdb=" O THR G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 154 Processing helix chain 'G' and resid 154 through 167 removed outlier: 4.157A pdb=" N VAL G 158 " --> pdb=" O LYS G 154 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE G 162 " --> pdb=" O VAL G 158 " (cutoff:3.500A) Proline residue: G 163 - end of helix Processing helix chain 'G' and resid 168 through 174 Processing helix chain 'G' and resid 192 through 227 removed outlier: 3.798A pdb=" N VAL G 196 " --> pdb=" O ASN G 192 " (cutoff:3.500A) Proline residue: G 211 - end of helix removed outlier: 3.780A pdb=" N SER G 227 " --> pdb=" O ILE G 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 267 Proline residue: G 254 - end of helix Processing helix chain 'G' and resid 274 through 291 removed outlier: 3.646A pdb=" N ASN G 278 " --> pdb=" O CYS G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 305 removed outlier: 4.394A pdb=" N ASN G 298 " --> pdb=" O HIS G 294 " (cutoff:3.500A) Proline residue: G 299 - end of helix removed outlier: 3.578A pdb=" N LEU G 305 " --> pdb=" O LEU G 301 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 64 removed outlier: 3.756A pdb=" N ILE R 39 " --> pdb=" O ASN R 35 " (cutoff:3.500A) Proline residue: R 42 - end of helix Processing helix chain 'R' and resid 72 through 90 removed outlier: 4.051A pdb=" N TYR R 76 " --> pdb=" O MET R 72 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N THR R 90 " --> pdb=" O LEU R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 100 removed outlier: 3.569A pdb=" N TRP R 94 " --> pdb=" O THR R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 139 removed outlier: 4.045A pdb=" N LEU R 120 " --> pdb=" O TYR R 116 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR R 121 " --> pdb=" O THR R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 154 Processing helix chain 'R' and resid 154 through 167 removed outlier: 4.099A pdb=" N VAL R 158 " --> pdb=" O LYS R 154 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE R 162 " --> pdb=" O VAL R 158 " (cutoff:3.500A) Proline residue: R 163 - end of helix Processing helix chain 'R' and resid 168 through 174 Processing helix chain 'R' and resid 192 through 227 removed outlier: 3.784A pdb=" N VAL R 196 " --> pdb=" O ASN R 192 " (cutoff:3.500A) Proline residue: R 211 - end of helix removed outlier: 3.688A pdb=" N SER R 227 " --> pdb=" O ILE R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 267 removed outlier: 3.759A pdb=" N THR R 241 " --> pdb=" O ALA R 237 " (cutoff:3.500A) Proline residue: R 254 - end of helix Processing helix chain 'R' and resid 274 through 291 removed outlier: 3.595A pdb=" N ASN R 278 " --> pdb=" O CYS R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 305 removed outlier: 4.263A pdb=" N ASN R 298 " --> pdb=" O HIS R 294 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 removed outlier: 3.661A pdb=" N SER A 36 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 2 through 4 Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 4 removed outlier: 3.807A pdb=" N SER B 36 " --> pdb=" O GLY B 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 175 through 180 removed outlier: 3.720A pdb=" N ASN C 176 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP C 187 " --> pdb=" O ASN C 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 2 through 8 removed outlier: 3.704A pdb=" N SER D 36 " --> pdb=" O GLY D 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 175 through 180 removed outlier: 3.797A pdb=" N ASN G 176 " --> pdb=" O ASP G 187 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP G 187 " --> pdb=" O ASN G 176 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 175 through 180 removed outlier: 3.720A pdb=" N ASN R 176 " --> pdb=" O ASP R 187 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP R 187 " --> pdb=" O ASN R 176 " (cutoff:3.500A) 622 hydrogen bonds defined for protein. 1827 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: 1.29 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1275 1.29 - 1.43: 2329 1.43 - 1.56: 5160 1.56 - 1.69: 3 1.69 - 1.83: 63 Bond restraints: 8830 Sorted by residual: bond pdb=" O22 D21 G 402 " pdb=" P23 D21 G 402 " ideal model delta sigma weight residual 1.723 1.629 0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C16 D21 C 402 " pdb=" O18 D21 C 402 " ideal model delta sigma weight residual 1.326 1.405 -0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C16 D21 R 402 " pdb=" O18 D21 R 402 " ideal model delta sigma weight residual 1.326 1.404 -0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C31 D21 R 402 " pdb=" O30 D21 R 402 " ideal model delta sigma weight residual 1.327 1.404 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" O22 D21 C 402 " pdb=" P23 D21 C 402 " ideal model delta sigma weight residual 1.723 1.647 0.076 2.00e-02 2.50e+03 1.44e+01 ... (remaining 8825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 11792 2.33 - 4.65: 92 4.65 - 6.98: 44 6.98 - 9.30: 9 9.30 - 11.63: 7 Bond angle restraints: 11944 Sorted by residual: angle pdb=" C20 D21 R 402 " pdb=" O30 D21 R 402 " pdb=" C31 D21 R 402 " ideal model delta sigma weight residual 125.41 113.78 11.63 3.00e+00 1.11e-01 1.50e+01 angle pdb=" N ILE G 39 " pdb=" CA ILE G 39 " pdb=" C ILE G 39 " ideal model delta sigma weight residual 112.96 109.24 3.72 1.00e+00 1.00e+00 1.38e+01 angle pdb=" C20 D21 C 402 " pdb=" O30 D21 C 402 " pdb=" C31 D21 C 402 " ideal model delta sigma weight residual 125.41 114.31 11.10 3.00e+00 1.11e-01 1.37e+01 angle pdb=" C34 D21 G 402 " pdb=" C35 D21 G 402 " pdb=" C36 D21 G 402 " ideal model delta sigma weight residual 113.18 102.32 10.86 3.00e+00 1.11e-01 1.31e+01 angle pdb=" N ILE R 39 " pdb=" CA ILE R 39 " pdb=" C ILE R 39 " ideal model delta sigma weight residual 112.96 109.36 3.60 1.00e+00 1.00e+00 1.29e+01 ... (remaining 11939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.41: 5158 28.41 - 56.81: 228 56.81 - 85.22: 18 85.22 - 113.62: 3 113.62 - 142.03: 6 Dihedral angle restraints: 5413 sinusoidal: 2356 harmonic: 3057 Sorted by residual: dihedral pdb=" CB CYS R 28 " pdb=" SG CYS R 28 " pdb=" SG CYS R 274 " pdb=" CB CYS R 274 " ideal model delta sinusoidal sigma weight residual 93.00 6.90 86.10 1 1.00e+01 1.00e-02 8.95e+01 dihedral pdb=" CB CYS C 28 " pdb=" SG CYS C 28 " pdb=" SG CYS C 274 " pdb=" CB CYS C 274 " ideal model delta sinusoidal sigma weight residual 93.00 13.54 79.46 1 1.00e+01 1.00e-02 7.84e+01 dihedral pdb=" CB CYS G 28 " pdb=" SG CYS G 28 " pdb=" SG CYS G 274 " pdb=" CB CYS G 274 " ideal model delta sinusoidal sigma weight residual 93.00 20.69 72.31 1 1.00e+01 1.00e-02 6.68e+01 ... (remaining 5410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1269 0.071 - 0.142: 110 0.142 - 0.213: 0 0.213 - 0.284: 1 0.284 - 0.355: 2 Chirality restraints: 1382 Sorted by residual: chirality pdb=" C20 D21 C 402 " pdb=" C19 D21 C 402 " pdb=" C21 D21 C 402 " pdb=" O30 D21 C 402 " both_signs ideal model delta sigma weight residual False 2.18 2.53 -0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C20 D21 R 402 " pdb=" C19 D21 R 402 " pdb=" C21 D21 R 402 " pdb=" O30 D21 R 402 " both_signs ideal model delta sigma weight residual False 2.18 2.52 -0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" C20 D21 G 402 " pdb=" C19 D21 G 402 " pdb=" C21 D21 G 402 " pdb=" O30 D21 G 402 " both_signs ideal model delta sigma weight residual False 2.18 2.44 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1379 not shown) Planarity restraints: 1408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL R 206 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.14e+00 pdb=" C VAL R 206 " 0.039 2.00e-02 2.50e+03 pdb=" O VAL R 206 " -0.015 2.00e-02 2.50e+03 pdb=" N GLY R 207 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 206 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.98e+00 pdb=" C VAL G 206 " -0.039 2.00e-02 2.50e+03 pdb=" O VAL G 206 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY G 207 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 206 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.76e+00 pdb=" C VAL C 206 " 0.038 2.00e-02 2.50e+03 pdb=" O VAL C 206 " -0.014 2.00e-02 2.50e+03 pdb=" N GLY C 207 " -0.013 2.00e-02 2.50e+03 ... (remaining 1405 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1809 2.78 - 3.31: 8194 3.31 - 3.84: 13362 3.84 - 4.37: 14176 4.37 - 4.90: 26572 Nonbonded interactions: 64113 Sorted by model distance: nonbonded pdb=" O GLY D 42 " pdb=" NH2 ARG G 30 " model vdw 2.254 3.120 nonbonded pdb=" NH2 ARG R 188 " pdb=" OH TYR R 190 " model vdw 2.255 3.120 nonbonded pdb=" NH2 ARG C 188 " pdb=" OH TYR C 190 " model vdw 2.280 3.120 nonbonded pdb=" O LEU C 165 " pdb=" OG1 THR C 168 " model vdw 2.281 3.040 nonbonded pdb=" O GLY B 42 " pdb=" NH2 ARG C 30 " model vdw 2.297 3.120 ... (remaining 64108 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' } ncs_group { reference = (chain 'C' and (resid 26 through 228 or resid 236 through 402)) selection = (chain 'G' and (resid 26 through 228 or resid 236 through 402)) selection = chain 'R' } 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: 2.160 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.530 Find NCS groups from input model: 0.160 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 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 : 0.004 0.094 8836 Z= 0.207 Angle : 0.711 11.630 11956 Z= 0.325 Chirality : 0.042 0.355 1382 Planarity : 0.004 0.035 1408 Dihedral : 15.860 142.026 3423 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % 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: 1.37 (0.27), residues: 1016 helix: 1.76 (0.19), residues: 763 sheet: 0.46 (0.63), residues: 80 loop : -2.86 (0.41), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 235 TYR 0.010 0.001 TYR A 39 PHE 0.015 0.001 PHE R 248 TRP 0.006 0.001 TRP C 102 HIS 0.003 0.001 HIS C 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.21 ( 8830) covalent geometry : angle 0.71007 / 0.32 (11944) SS BOND : bond 0.00223 / 0.13 ( 6) SS BOND : angle 1.55112 / 1.10 ( 12) hydrogen bonds : bond 0.09402 / 6.23 ( 618) hydrogen bonds : angle 4.90079 / 3.56 ( 1827) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 TYR cc_start: 0.7868 (m-80) cc_final: 0.7544 (m-80) REVERT: C 219 TYR cc_start: 0.7826 (m-10) cc_final: 0.7207 (m-80) REVERT: C 304 PHE cc_start: 0.7950 (m-80) cc_final: 0.7729 (m-80) REVERT: D 64 LYS cc_start: 0.8744 (mttp) cc_final: 0.8373 (mmtm) REVERT: R 94 TRP cc_start: 0.7718 (m100) cc_final: 0.7496 (m100) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.0794 time to fit residues: 27.4679 Evaluate side-chains 187 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.171049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.150849 restraints weight = 11117.568| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.01 r_work: 0.3631 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8836 Z= 0.149 Angle : 0.567 7.308 11956 Z= 0.294 Chirality : 0.040 0.140 1382 Planarity : 0.004 0.036 1408 Dihedral : 14.058 144.372 1453 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.52 % Allowed : 10.98 % Favored : 87.50 % 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: 1.16 (0.27), residues: 1016 helix: 1.60 (0.19), residues: 775 sheet: -0.02 (0.58), residues: 83 loop : -2.99 (0.40), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 188 TYR 0.012 0.001 TYR A 13 PHE 0.030 0.002 PHE C 248 TRP 0.006 0.001 TRP R 283 HIS 0.004 0.001 HIS R 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 8830) covalent geometry : angle 0.56569 / 0.29 (11944) SS BOND : bond 0.00187 / 0.14 ( 6) SS BOND : angle 1.25482 / 0.84 ( 12) hydrogen bonds : bond 0.04975 / 3.20 ( 618) hydrogen bonds : angle 4.41124 / 3.17 ( 1827) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 191 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ILE cc_start: 0.7337 (mt) cc_final: 0.7068 (pt) REVERT: B 37 TYR cc_start: 0.8091 (m-80) cc_final: 0.7862 (m-80) REVERT: C 125 LEU cc_start: 0.8158 (mm) cc_final: 0.7772 (mp) REVERT: C 219 TYR cc_start: 0.7983 (m-10) cc_final: 0.7627 (m-80) REVERT: D 35 ILE cc_start: 0.7209 (mt) cc_final: 0.6942 (pt) REVERT: G 145 GLN cc_start: 0.8093 (tp-100) cc_final: 0.7692 (mp10) REVERT: G 219 TYR cc_start: 0.7998 (m-10) cc_final: 0.7716 (m-10) REVERT: R 145 GLN cc_start: 0.7880 (tp-100) cc_final: 0.7483 (mp10) outliers start: 14 outliers final: 11 residues processed: 199 average time/residue: 0.0737 time to fit residues: 21.5113 Evaluate side-chains 194 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 183 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain G residue 238 LEU Chi-restraints excluded: chain G residue 290 LEU Chi-restraints excluded: chain R residue 138 ILE Chi-restraints excluded: chain R residue 224 SER Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 92 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.0980 chunk 84 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 66 optimal weight: 0.0770 chunk 28 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 281 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.170378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.150332 restraints weight = 10844.846| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.99 r_work: 0.3646 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8836 Z= 0.142 Angle : 0.548 10.264 11956 Z= 0.288 Chirality : 0.040 0.157 1382 Planarity : 0.004 0.043 1408 Dihedral : 13.222 138.539 1453 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.28 % Allowed : 13.04 % Favored : 84.67 % 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: 1.05 (0.27), residues: 1016 helix: 1.54 (0.19), residues: 778 sheet: -0.37 (0.54), residues: 93 loop : -3.20 (0.39), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 188 TYR 0.017 0.001 TYR D 13 PHE 0.037 0.001 PHE C 248 TRP 0.007 0.001 TRP R 94 HIS 0.004 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 8830) covalent geometry : angle 0.54518 / 0.29 (11944) SS BOND : bond 0.00248 / 0.15 ( 6) SS BOND : angle 1.91933 / 1.31 ( 12) hydrogen bonds : bond 0.04934 / 3.19 ( 618) hydrogen bonds : angle 4.30043 / 3.09 ( 1827) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6926 (OUTLIER) cc_final: 0.6647 (tpt) REVERT: A 35 ILE cc_start: 0.7299 (mt) cc_final: 0.7081 (pt) REVERT: A 41 ASN cc_start: 0.7534 (t0) cc_final: 0.7244 (t0) REVERT: C 219 TYR cc_start: 0.8009 (m-10) cc_final: 0.7753 (m-80) REVERT: D 35 ILE cc_start: 0.7165 (mt) cc_final: 0.6941 (pt) REVERT: G 145 GLN cc_start: 0.7998 (tp-100) cc_final: 0.7597 (mp10) REVERT: R 145 GLN cc_start: 0.7819 (tp-100) cc_final: 0.7520 (mp10) outliers start: 21 outliers final: 19 residues processed: 202 average time/residue: 0.0762 time to fit residues: 22.6215 Evaluate side-chains 199 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 172 PHE Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain G residue 238 LEU Chi-restraints excluded: chain G residue 290 LEU Chi-restraints excluded: chain R residue 129 PHE Chi-restraints excluded: chain R residue 138 ILE Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 243 ILE Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 269 ILE Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 61 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 74 optimal weight: 0.1980 chunk 6 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.170038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.149933 restraints weight = 11072.061| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.02 r_work: 0.3633 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8836 Z= 0.142 Angle : 0.553 7.711 11956 Z= 0.286 Chirality : 0.040 0.176 1382 Planarity : 0.004 0.042 1408 Dihedral : 12.701 133.503 1453 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.39 % Allowed : 15.54 % Favored : 82.07 % 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: 1.05 (0.27), residues: 1016 helix: 1.51 (0.19), residues: 778 sheet: -0.25 (0.56), residues: 90 loop : -3.04 (0.40), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 188 TYR 0.017 0.001 TYR D 13 PHE 0.038 0.001 PHE C 248 TRP 0.007 0.001 TRP R 94 HIS 0.004 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 8830) covalent geometry : angle 0.55111 / 0.29 (11944) SS BOND : bond 0.00200 / 0.13 ( 6) SS BOND : angle 1.51127 / 1.00 ( 12) hydrogen bonds : bond 0.04873 / 3.15 ( 618) hydrogen bonds : angle 4.29623 / 3.08 ( 1827) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ILE cc_start: 0.7316 (mt) cc_final: 0.7035 (pt) REVERT: A 41 ASN cc_start: 0.7600 (t0) cc_final: 0.7306 (t0) REVERT: C 149 LYS cc_start: 0.6961 (ttmt) cc_final: 0.6723 (tttt) REVERT: C 219 TYR cc_start: 0.8005 (m-10) cc_final: 0.7723 (m-80) REVERT: D 35 ILE cc_start: 0.7189 (mt) cc_final: 0.6942 (pt) REVERT: G 145 GLN cc_start: 0.8000 (tp-100) cc_final: 0.7662 (mp10) REVERT: R 145 GLN cc_start: 0.7995 (tp-100) cc_final: 0.7516 (mp10) outliers start: 22 outliers final: 16 residues processed: 197 average time/residue: 0.0716 time to fit residues: 20.9619 Evaluate side-chains 197 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 172 PHE Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain G residue 238 LEU Chi-restraints excluded: chain G residue 290 LEU Chi-restraints excluded: chain R residue 129 PHE Chi-restraints excluded: chain R residue 138 ILE Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 224 SER Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 5 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.167929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.147901 restraints weight = 10935.158| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.99 r_work: 0.3612 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8836 Z= 0.169 Angle : 0.572 7.002 11956 Z= 0.296 Chirality : 0.041 0.193 1382 Planarity : 0.004 0.045 1408 Dihedral : 12.604 130.277 1453 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.72 % Allowed : 17.07 % Favored : 80.22 % 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: 0.96 (0.27), residues: 1016 helix: 1.44 (0.19), residues: 776 sheet: -0.21 (0.56), residues: 90 loop : -3.08 (0.40), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 188 TYR 0.021 0.001 TYR A 13 PHE 0.034 0.002 PHE C 248 TRP 0.008 0.001 TRP R 94 HIS 0.006 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 ( 8830) covalent geometry : angle 0.57084 / 0.30 (11944) SS BOND : bond 0.00261 / 0.17 ( 6) SS BOND : angle 1.34715 / 0.94 ( 12) hydrogen bonds : bond 0.05221 / 3.38 ( 618) hydrogen bonds : angle 4.35518 / 3.12 ( 1827) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ILE cc_start: 0.7259 (mt) cc_final: 0.7039 (pt) REVERT: A 41 ASN cc_start: 0.7707 (t0) cc_final: 0.7397 (t0) REVERT: B 64 LYS cc_start: 0.8719 (mttp) cc_final: 0.8313 (mmtm) REVERT: C 125 LEU cc_start: 0.8278 (mm) cc_final: 0.7991 (mp) REVERT: C 219 TYR cc_start: 0.8021 (m-10) cc_final: 0.7702 (m-80) REVERT: D 35 ILE cc_start: 0.7124 (mt) cc_final: 0.6899 (pt) REVERT: G 145 GLN cc_start: 0.8053 (tp-100) cc_final: 0.7699 (mp10) REVERT: R 145 GLN cc_start: 0.7999 (tp-100) cc_final: 0.7553 (mp10) REVERT: R 156 VAL cc_start: 0.7286 (OUTLIER) cc_final: 0.7058 (t) outliers start: 25 outliers final: 17 residues processed: 197 average time/residue: 0.0667 time to fit residues: 19.3868 Evaluate side-chains 197 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 172 PHE Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain G residue 290 LEU Chi-restraints excluded: chain R residue 129 PHE Chi-restraints excluded: chain R residue 138 ILE Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 224 SER Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 0 optimal weight: 3.9990 chunk 12 optimal weight: 0.0980 chunk 27 optimal weight: 0.0040 chunk 82 optimal weight: 0.0870 chunk 85 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 6 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.2170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.168664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.148614 restraints weight = 11668.215| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.01 r_work: 0.3619 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8836 Z= 0.114 Angle : 0.536 7.746 11956 Z= 0.272 Chirality : 0.039 0.191 1382 Planarity : 0.004 0.038 1408 Dihedral : 11.776 121.086 1453 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.07 % Allowed : 19.24 % Favored : 78.70 % 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: 1.23 (0.27), residues: 1016 helix: 1.62 (0.19), residues: 768 sheet: -0.05 (0.56), residues: 90 loop : -2.71 (0.41), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 40 TYR 0.018 0.001 TYR D 13 PHE 0.032 0.001 PHE R 248 TRP 0.007 0.001 TRP R 94 HIS 0.003 0.001 HIS C 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 ( 8830) covalent geometry : angle 0.53354 / 0.27 (11944) SS BOND : bond 0.00330 / 0.14 ( 6) SS BOND : angle 1.59996 / 1.25 ( 12) hydrogen bonds : bond 0.04272 / 2.76 ( 618) hydrogen bonds : angle 4.25375 / 3.04 ( 1827) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 TYR cc_start: 0.6919 (t80) cc_final: 0.6717 (t80) REVERT: A 35 ILE cc_start: 0.7210 (mt) cc_final: 0.6948 (pt) REVERT: A 41 ASN cc_start: 0.7745 (t0) cc_final: 0.7460 (t0) REVERT: C 219 TYR cc_start: 0.7921 (m-10) cc_final: 0.7628 (m-80) REVERT: G 145 GLN cc_start: 0.8072 (tp-100) cc_final: 0.7727 (mp10) REVERT: G 172 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.6658 (t80) REVERT: G 219 TYR cc_start: 0.7953 (m-10) cc_final: 0.7694 (m-80) REVERT: R 145 GLN cc_start: 0.7970 (tp-100) cc_final: 0.7556 (mp10) outliers start: 19 outliers final: 14 residues processed: 195 average time/residue: 0.0645 time to fit residues: 19.0212 Evaluate side-chains 190 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 172 PHE Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain G residue 238 LEU Chi-restraints excluded: chain G residue 290 LEU Chi-restraints excluded: chain R residue 129 PHE Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 201 PHE Chi-restraints excluded: chain R residue 224 SER Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 81 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 64 optimal weight: 0.1980 chunk 84 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 95 optimal weight: 0.4980 chunk 66 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.166528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.146223 restraints weight = 11654.436| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.99 r_work: 0.3619 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8836 Z= 0.136 Angle : 0.565 8.867 11956 Z= 0.286 Chirality : 0.040 0.216 1382 Planarity : 0.004 0.039 1408 Dihedral : 11.889 119.079 1453 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.39 % Allowed : 18.80 % Favored : 78.80 % 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: 1.21 (0.27), residues: 1016 helix: 1.57 (0.19), residues: 770 sheet: 0.04 (0.57), residues: 90 loop : -2.63 (0.42), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 188 TYR 0.020 0.001 TYR R 135 PHE 0.033 0.001 PHE R 248 TRP 0.008 0.001 TRP R 94 HIS 0.005 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 8830) covalent geometry : angle 0.56344 / 0.28 (11944) SS BOND : bond 0.00225 / 0.14 ( 6) SS BOND : angle 1.53912 / 1.20 ( 12) hydrogen bonds : bond 0.04646 / 3.00 ( 618) hydrogen bonds : angle 4.28656 / 3.06 ( 1827) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ILE cc_start: 0.7153 (mt) cc_final: 0.6930 (pt) REVERT: A 41 ASN cc_start: 0.7776 (t0) cc_final: 0.7503 (t0) REVERT: B 64 LYS cc_start: 0.8729 (mttp) cc_final: 0.8322 (mmtm) REVERT: C 125 LEU cc_start: 0.8349 (mm) cc_final: 0.7945 (mp) REVERT: C 219 TYR cc_start: 0.7982 (m-10) cc_final: 0.7717 (m-80) REVERT: G 145 GLN cc_start: 0.8047 (tp-100) cc_final: 0.7717 (mp10) REVERT: G 172 PHE cc_start: 0.7562 (OUTLIER) cc_final: 0.6652 (t80) REVERT: R 145 GLN cc_start: 0.7952 (tp-100) cc_final: 0.7574 (mp10) outliers start: 22 outliers final: 15 residues processed: 202 average time/residue: 0.0681 time to fit residues: 20.3034 Evaluate side-chains 201 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 172 PHE Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 290 LEU Chi-restraints excluded: chain R residue 129 PHE Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 201 PHE Chi-restraints excluded: chain R residue 224 SER Chi-restraints excluded: chain R residue 243 ILE Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 41 optimal weight: 3.9990 chunk 60 optimal weight: 0.0470 chunk 72 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.164791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.144375 restraints weight = 11468.126| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.97 r_work: 0.3588 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 8836 Z= 0.163 Angle : 0.594 8.362 11956 Z= 0.303 Chirality : 0.041 0.230 1382 Planarity : 0.004 0.039 1408 Dihedral : 12.000 121.132 1453 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.85 % Allowed : 19.67 % Favored : 78.48 % 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: 0.99 (0.27), residues: 1016 helix: 1.44 (0.19), residues: 775 sheet: -0.09 (0.56), residues: 90 loop : -2.95 (0.40), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 188 TYR 0.018 0.001 TYR D 13 PHE 0.033 0.001 PHE R 248 TRP 0.009 0.001 TRP R 94 HIS 0.005 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 8830) covalent geometry : angle 0.59290 / 0.30 (11944) SS BOND : bond 0.00259 / 0.16 ( 6) SS BOND : angle 1.45733 / 1.09 ( 12) hydrogen bonds : bond 0.05041 / 3.26 ( 618) hydrogen bonds : angle 4.37594 / 3.12 ( 1827) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 187 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ILE cc_start: 0.7188 (mt) cc_final: 0.6892 (pt) REVERT: A 41 ASN cc_start: 0.7814 (t0) cc_final: 0.7548 (t0) REVERT: B 64 LYS cc_start: 0.8727 (mttp) cc_final: 0.8312 (mmtm) REVERT: C 125 LEU cc_start: 0.8351 (mm) cc_final: 0.7971 (mp) REVERT: C 219 TYR cc_start: 0.7984 (m-10) cc_final: 0.7661 (m-80) REVERT: D 41 ASN cc_start: 0.7688 (t0) cc_final: 0.7304 (t0) REVERT: G 145 GLN cc_start: 0.8054 (tp-100) cc_final: 0.7722 (mp10) REVERT: G 172 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.6686 (t80) REVERT: R 145 GLN cc_start: 0.7984 (tp-100) cc_final: 0.7541 (mp10) outliers start: 17 outliers final: 13 residues processed: 193 average time/residue: 0.0649 time to fit residues: 18.3666 Evaluate side-chains 197 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 183 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 172 PHE Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain G residue 290 LEU Chi-restraints excluded: chain R residue 129 PHE Chi-restraints excluded: chain R residue 138 ILE Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 224 SER Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 8 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 50 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.165582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.145197 restraints weight = 11459.675| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.99 r_work: 0.3601 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8836 Z= 0.149 Angle : 0.587 8.305 11956 Z= 0.299 Chirality : 0.041 0.227 1382 Planarity : 0.004 0.035 1408 Dihedral : 11.788 120.658 1453 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.74 % Allowed : 20.54 % Favored : 77.72 % 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: 1.05 (0.27), residues: 1016 helix: 1.47 (0.19), residues: 770 sheet: -0.15 (0.55), residues: 90 loop : -2.62 (0.42), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 188 TYR 0.019 0.001 TYR R 135 PHE 0.029 0.001 PHE R 248 TRP 0.009 0.001 TRP R 94 HIS 0.003 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 8830) covalent geometry : angle 0.58600 / 0.30 (11944) SS BOND : bond 0.00230 / 0.14 ( 6) SS BOND : angle 1.38623 / 1.02 ( 12) hydrogen bonds : bond 0.04910 / 3.17 ( 618) hydrogen bonds : angle 4.38816 / 3.13 ( 1827) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ILE cc_start: 0.7168 (mt) cc_final: 0.6909 (pt) REVERT: A 41 ASN cc_start: 0.7822 (t0) cc_final: 0.7580 (t0) REVERT: B 64 LYS cc_start: 0.8707 (mttp) cc_final: 0.8248 (mmtm) REVERT: C 125 LEU cc_start: 0.8351 (mm) cc_final: 0.7959 (mp) REVERT: C 219 TYR cc_start: 0.7969 (m-10) cc_final: 0.7667 (m-80) REVERT: D 41 ASN cc_start: 0.7708 (t0) cc_final: 0.7348 (t0) REVERT: G 145 GLN cc_start: 0.8099 (tp-100) cc_final: 0.7727 (mp10) REVERT: G 172 PHE cc_start: 0.7574 (OUTLIER) cc_final: 0.6698 (t80) REVERT: R 145 GLN cc_start: 0.8022 (tp-100) cc_final: 0.7582 (mp10) outliers start: 16 outliers final: 15 residues processed: 192 average time/residue: 0.0723 time to fit residues: 20.5772 Evaluate side-chains 199 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 172 PHE Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain G residue 290 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 224 SER Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 99 optimal weight: 0.0870 chunk 38 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 98 optimal weight: 0.0370 chunk 11 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.166414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.145977 restraints weight = 11558.050| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.99 r_work: 0.3618 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8836 Z= 0.136 Angle : 0.580 8.973 11956 Z= 0.294 Chirality : 0.040 0.223 1382 Planarity : 0.004 0.034 1408 Dihedral : 11.496 118.965 1453 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.74 % Allowed : 20.54 % Favored : 77.72 % 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: 1.25 (0.27), residues: 1016 helix: 1.59 (0.19), residues: 763 sheet: -0.16 (0.55), residues: 90 loop : -2.18 (0.46), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 77 TYR 0.019 0.001 TYR R 135 PHE 0.027 0.001 PHE C 248 TRP 0.009 0.001 TRP R 94 HIS 0.003 0.001 HIS C 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 8830) covalent geometry : angle 0.57869 / 0.29 (11944) SS BOND : bond 0.00217 / 0.13 ( 6) SS BOND : angle 1.34249 / 0.98 ( 12) hydrogen bonds : bond 0.04720 / 3.05 ( 618) hydrogen bonds : angle 4.35040 / 3.10 ( 1827) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 188 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ILE cc_start: 0.7144 (mt) cc_final: 0.6895 (pt) REVERT: A 41 ASN cc_start: 0.7811 (t0) cc_final: 0.7445 (t0) REVERT: B 60 LYS cc_start: 0.7692 (mtpt) cc_final: 0.6977 (mtmm) REVERT: B 64 LYS cc_start: 0.8700 (mttp) cc_final: 0.8245 (mmtm) REVERT: C 125 LEU cc_start: 0.8341 (mm) cc_final: 0.7938 (mp) REVERT: C 219 TYR cc_start: 0.7994 (m-10) cc_final: 0.7721 (m-80) REVERT: D 41 ASN cc_start: 0.7709 (t0) cc_final: 0.7373 (t0) REVERT: G 145 GLN cc_start: 0.8104 (tp-100) cc_final: 0.7740 (mp10) REVERT: G 172 PHE cc_start: 0.7544 (OUTLIER) cc_final: 0.6694 (t80) REVERT: R 145 GLN cc_start: 0.8063 (tp-100) cc_final: 0.7563 (mp10) outliers start: 16 outliers final: 12 residues processed: 195 average time/residue: 0.0633 time to fit residues: 18.4219 Evaluate side-chains 196 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 183 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 172 PHE Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain G residue 290 LEU Chi-restraints excluded: chain R residue 224 SER Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 9 optimal weight: 6.9990 chunk 50 optimal weight: 0.4980 chunk 63 optimal weight: 0.9980 chunk 23 optimal weight: 0.0980 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 0.0770 chunk 87 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.166978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.146571 restraints weight = 11609.477| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.00 r_work: 0.3620 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8836 Z= 0.130 Angle : 0.578 9.195 11956 Z= 0.293 Chirality : 0.040 0.222 1382 Planarity : 0.004 0.034 1408 Dihedral : 11.240 117.299 1453 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.07 % Allowed : 20.22 % Favored : 77.72 % 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: 1.27 (0.27), residues: 1016 helix: 1.60 (0.19), residues: 763 sheet: -0.16 (0.54), residues: 90 loop : -2.18 (0.46), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 77 TYR 0.014 0.001 TYR D 13 PHE 0.027 0.001 PHE C 248 TRP 0.008 0.001 TRP R 94 HIS 0.003 0.001 HIS C 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 8830) covalent geometry : angle 0.57674 / 0.29 (11944) SS BOND : bond 0.00203 / 0.12 ( 6) SS BOND : angle 1.30424 / 0.95 ( 12) hydrogen bonds : bond 0.04578 / 2.95 ( 618) hydrogen bonds : angle 4.32189 / 3.08 ( 1827) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1858.46 seconds wall clock time: 32 minutes 36.80 seconds (1956.80 seconds total)