Starting phenix.real_space_refine on Wed Mar 4 09:21:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l6u_23208/03_2026/7l6u_23208.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l6u_23208/03_2026/7l6u_23208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7l6u_23208/03_2026/7l6u_23208.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l6u_23208/03_2026/7l6u_23208.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l6u_23208/03_2026/7l6u_23208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l6u_23208/03_2026/7l6u_23208.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.003 sd= 0.064 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: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 8255 2.51 5 N 2115 2.21 5 O 2275 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 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: 12675 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2535 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 14, 'TRANS': 296} Chain: "B" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2535 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 14, 'TRANS': 296} Chain: "C" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2535 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 14, 'TRANS': 296} Chain: "D" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2535 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 14, 'TRANS': 296} Chain: "E" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2535 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 14, 'TRANS': 296} Time building chain proxies: 2.87, per 1000 atoms: 0.23 Number of scatterers: 12675 At special positions: 0 Unit cell: (92.064, 93.16, 121.656, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 2275 8.00 N 2115 7.00 C 8255 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: 0.91 Conformation dependent library (CDL) restraints added in 542.6 milliseconds 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2940 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 15 sheets defined 38.3% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 50 through 54 removed outlier: 3.928A pdb=" N LYS A 54 " --> pdb=" O PRO A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.663A pdb=" N ASN A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'A' and resid 202 through 207 Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 227 through 253 removed outlier: 3.833A pdb=" N PHE A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR A 237 " --> pdb=" O GLN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 285 removed outlier: 3.709A pdb=" N GLN A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 321 removed outlier: 4.261A pdb=" N GLN A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Proline residue: A 305 - end of helix removed outlier: 3.541A pdb=" N THR A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 54 removed outlier: 3.928A pdb=" N LYS B 54 " --> pdb=" O PRO B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 68 removed outlier: 3.663A pdb=" N ASN B 68 " --> pdb=" O GLU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'B' and resid 202 through 207 Processing helix chain 'B' and resid 209 through 220 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 227 through 253 removed outlier: 3.833A pdb=" N PHE B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR B 237 " --> pdb=" O GLN B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 285 removed outlier: 3.709A pdb=" N GLN B 264 " --> pdb=" O THR B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 321 removed outlier: 4.261A pdb=" N GLN B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 305 - end of helix removed outlier: 3.541A pdb=" N THR B 321 " --> pdb=" O ILE B 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 54 removed outlier: 3.928A pdb=" N LYS C 54 " --> pdb=" O PRO C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 68 removed outlier: 3.663A pdb=" N ASN C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'C' and resid 202 through 207 Processing helix chain 'C' and resid 209 through 220 Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 227 through 253 removed outlier: 3.833A pdb=" N PHE C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR C 237 " --> pdb=" O GLN C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 285 removed outlier: 3.710A pdb=" N GLN C 264 " --> pdb=" O THR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 321 removed outlier: 4.260A pdb=" N GLN C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Proline residue: C 305 - end of helix removed outlier: 3.541A pdb=" N THR C 321 " --> pdb=" O ILE C 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 54 removed outlier: 3.928A pdb=" N LYS D 54 " --> pdb=" O PRO D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 68 removed outlier: 3.664A pdb=" N ASN D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 121 Processing helix chain 'D' and resid 202 through 207 Processing helix chain 'D' and resid 209 through 220 Processing helix chain 'D' and resid 221 through 225 Processing helix chain 'D' and resid 227 through 253 removed outlier: 3.832A pdb=" N PHE D 236 " --> pdb=" O LEU D 232 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR D 237 " --> pdb=" O GLN D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 285 removed outlier: 3.710A pdb=" N GLN D 264 " --> pdb=" O THR D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 321 removed outlier: 4.261A pdb=" N GLN D 298 " --> pdb=" O ASP D 294 " (cutoff:3.500A) Proline residue: D 305 - end of helix removed outlier: 3.541A pdb=" N THR D 321 " --> pdb=" O ILE D 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 54 removed outlier: 3.928A pdb=" N LYS E 54 " --> pdb=" O PRO E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 68 removed outlier: 3.663A pdb=" N ASN E 68 " --> pdb=" O GLU E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 121 Processing helix chain 'E' and resid 202 through 207 Processing helix chain 'E' and resid 209 through 220 Processing helix chain 'E' and resid 221 through 225 Processing helix chain 'E' and resid 227 through 253 removed outlier: 3.833A pdb=" N PHE E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR E 237 " --> pdb=" O GLN E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 285 removed outlier: 3.710A pdb=" N GLN E 264 " --> pdb=" O THR E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 321 removed outlier: 4.260A pdb=" N GLN E 298 " --> pdb=" O ASP E 294 " (cutoff:3.500A) Proline residue: E 305 - end of helix removed outlier: 3.541A pdb=" N THR E 321 " --> pdb=" O ILE E 317 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.286A pdb=" N THR A 32 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY A 25 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL A 14 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER A 143 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL A 16 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE A 145 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE A 18 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.780A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.780A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 56 through 58 removed outlier: 6.285A pdb=" N THR B 32 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY B 25 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL B 14 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N SER B 143 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL B 16 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE B 145 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE B 18 " --> pdb=" O ILE B 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.779A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.779A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 58 removed outlier: 6.285A pdb=" N THR C 32 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY C 25 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL C 14 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER C 143 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL C 16 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE C 145 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE C 18 " --> pdb=" O ILE C 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.779A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.779A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 56 through 58 removed outlier: 6.285A pdb=" N THR D 32 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY D 25 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE D 23 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASP D 36 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL D 14 " --> pdb=" O ARG D 141 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER D 143 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL D 16 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE D 145 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE D 18 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.779A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.779A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 56 through 58 removed outlier: 6.286A pdb=" N THR E 32 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY E 25 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL E 14 " --> pdb=" O ARG E 141 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER E 143 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL E 16 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE E 145 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE E 18 " --> pdb=" O ILE E 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.779A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.779A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) 665 hydrogen bonds defined for protein. 1905 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: 1.99 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3037 1.33 - 1.45: 2787 1.45 - 1.57: 7141 1.57 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 13015 Sorted by residual: bond pdb=" C VAL A 58 " pdb=" N GLU A 59 " ideal model delta sigma weight residual 1.332 1.221 0.112 1.40e-02 5.10e+03 6.36e+01 bond pdb=" C VAL C 58 " pdb=" N GLU C 59 " ideal model delta sigma weight residual 1.332 1.222 0.111 1.40e-02 5.10e+03 6.23e+01 bond pdb=" C VAL D 58 " pdb=" N GLU D 59 " ideal model delta sigma weight residual 1.332 1.222 0.110 1.40e-02 5.10e+03 6.19e+01 bond pdb=" C VAL E 58 " pdb=" N GLU E 59 " ideal model delta sigma weight residual 1.332 1.223 0.110 1.40e-02 5.10e+03 6.13e+01 bond pdb=" C VAL B 58 " pdb=" N GLU B 59 " ideal model delta sigma weight residual 1.332 1.223 0.109 1.40e-02 5.10e+03 6.11e+01 ... (remaining 13010 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 17049 1.66 - 3.31: 519 3.31 - 4.97: 112 4.97 - 6.62: 50 6.62 - 8.28: 5 Bond angle restraints: 17735 Sorted by residual: angle pdb=" N VAL A 291 " pdb=" CA VAL A 291 " pdb=" C VAL A 291 " ideal model delta sigma weight residual 113.71 107.58 6.13 9.50e-01 1.11e+00 4.17e+01 angle pdb=" N VAL B 291 " pdb=" CA VAL B 291 " pdb=" C VAL B 291 " ideal model delta sigma weight residual 113.71 107.61 6.10 9.50e-01 1.11e+00 4.12e+01 angle pdb=" N VAL E 291 " pdb=" CA VAL E 291 " pdb=" C VAL E 291 " ideal model delta sigma weight residual 113.71 107.62 6.09 9.50e-01 1.11e+00 4.11e+01 angle pdb=" N VAL D 291 " pdb=" CA VAL D 291 " pdb=" C VAL D 291 " ideal model delta sigma weight residual 113.71 107.63 6.08 9.50e-01 1.11e+00 4.10e+01 angle pdb=" N VAL C 291 " pdb=" CA VAL C 291 " pdb=" C VAL C 291 " ideal model delta sigma weight residual 113.71 107.64 6.07 9.50e-01 1.11e+00 4.09e+01 ... (remaining 17730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 6653 15.94 - 31.89: 751 31.89 - 47.83: 175 47.83 - 63.78: 26 63.78 - 79.72: 10 Dihedral angle restraints: 7615 sinusoidal: 3060 harmonic: 4555 Sorted by residual: dihedral pdb=" CA GLN C 182 " pdb=" C GLN C 182 " pdb=" N PRO C 183 " pdb=" CA PRO C 183 " ideal model delta harmonic sigma weight residual 180.00 152.70 27.30 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA GLN A 182 " pdb=" C GLN A 182 " pdb=" N PRO A 183 " pdb=" CA PRO A 183 " ideal model delta harmonic sigma weight residual 180.00 152.70 27.30 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA GLN D 182 " pdb=" C GLN D 182 " pdb=" N PRO D 183 " pdb=" CA PRO D 183 " ideal model delta harmonic sigma weight residual 180.00 152.71 27.29 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 7612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1519 0.059 - 0.117: 396 0.117 - 0.176: 55 0.176 - 0.235: 0 0.235 - 0.293: 5 Chirality restraints: 1975 Sorted by residual: chirality pdb=" CA GLU B 59 " pdb=" N GLU B 59 " pdb=" C GLU B 59 " pdb=" CB GLU B 59 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA GLU D 59 " pdb=" N GLU D 59 " pdb=" C GLU D 59 " pdb=" CB GLU D 59 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA GLU A 59 " pdb=" N GLU A 59 " pdb=" C GLU A 59 " pdb=" CB GLU A 59 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 1972 not shown) Planarity restraints: 2260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 59 " -0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C GLU A 59 " 0.064 2.00e-02 2.50e+03 pdb=" O GLU A 59 " -0.024 2.00e-02 2.50e+03 pdb=" N ASN A 60 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 59 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C GLU B 59 " 0.064 2.00e-02 2.50e+03 pdb=" O GLU B 59 " -0.024 2.00e-02 2.50e+03 pdb=" N ASN B 60 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 59 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C GLU E 59 " 0.064 2.00e-02 2.50e+03 pdb=" O GLU E 59 " -0.024 2.00e-02 2.50e+03 pdb=" N ASN E 60 " -0.021 2.00e-02 2.50e+03 ... (remaining 2257 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 4737 2.87 - 3.38: 11474 3.38 - 3.89: 19850 3.89 - 4.39: 22253 4.39 - 4.90: 40341 Nonbonded interactions: 98655 Sorted by model distance: nonbonded pdb=" OH TYR D 33 " pdb=" O VAL D 127 " model vdw 2.365 3.040 nonbonded pdb=" OH TYR E 33 " pdb=" O VAL E 127 " model vdw 2.365 3.040 nonbonded pdb=" OH TYR A 33 " pdb=" O VAL A 127 " model vdw 2.365 3.040 nonbonded pdb=" OH TYR B 33 " pdb=" O VAL B 127 " model vdw 2.365 3.040 nonbonded pdb=" OH TYR C 33 " pdb=" O VAL C 127 " model vdw 2.366 3.040 ... (remaining 98650 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: 0.720 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: 0.040 Process input model: 11.890 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 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 : 0.009 0.112 13015 Z= 0.391 Angle : 0.786 8.281 17735 Z= 0.454 Chirality : 0.054 0.293 1975 Planarity : 0.005 0.070 2260 Dihedral : 14.086 79.721 4675 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 0.72 % Allowed : 0.79 % Favored : 98.49 % 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: -1.06 (0.22), residues: 1545 helix: 0.42 (0.22), residues: 515 sheet: -0.18 (0.26), residues: 480 loop : -2.25 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 199 TYR 0.021 0.002 TYR A 248 PHE 0.025 0.002 PHE B 247 TRP 0.009 0.001 TRP A 160 HIS 0.003 0.001 HIS D 285 Details of bonding type rmsd covalent geometry : bond 0.00905 (13015) covalent geometry : angle 0.78587 (17735) hydrogen bonds : bond 0.13090 ( 615) hydrogen bonds : angle 5.88600 ( 1905) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.469 Fit side-chains REVERT: A 142 PHE cc_start: 0.6837 (t80) cc_final: 0.6603 (t80) REVERT: B 138 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: B 142 PHE cc_start: 0.6826 (t80) cc_final: 0.6556 (t80) REVERT: C 142 PHE cc_start: 0.7021 (t80) cc_final: 0.6643 (t80) REVERT: D 142 PHE cc_start: 0.6975 (t80) cc_final: 0.6680 (t80) REVERT: E 138 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8182 (tt0) REVERT: E 142 PHE cc_start: 0.6831 (t80) cc_final: 0.6586 (t80) outliers start: 10 outliers final: 5 residues processed: 117 average time/residue: 0.1476 time to fit residues: 23.8549 Evaluate side-chains 90 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 59 GLU Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 138 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.166225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.132655 restraints weight = 14399.958| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.20 r_work: 0.3657 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13015 Z= 0.129 Angle : 0.593 7.036 17735 Z= 0.307 Chirality : 0.046 0.154 1975 Planarity : 0.004 0.054 2260 Dihedral : 5.919 55.543 1731 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.22 % Allowed : 4.17 % Favored : 95.61 % 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: -0.40 (0.23), residues: 1545 helix: 0.96 (0.23), residues: 535 sheet: 0.26 (0.26), residues: 480 loop : -2.05 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 255 TYR 0.015 0.001 TYR A 248 PHE 0.029 0.001 PHE E 247 TRP 0.005 0.001 TRP D 43 HIS 0.008 0.002 HIS E 285 Details of bonding type rmsd covalent geometry : bond 0.00292 (13015) covalent geometry : angle 0.59299 (17735) hydrogen bonds : bond 0.04060 ( 615) hydrogen bonds : angle 4.30756 ( 1905) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 0.456 Fit side-chains REVERT: A 142 PHE cc_start: 0.7179 (t80) cc_final: 0.6871 (t80) REVERT: B 109 SER cc_start: 0.8593 (p) cc_final: 0.8356 (p) REVERT: B 113 ASP cc_start: 0.7717 (m-30) cc_final: 0.7327 (p0) REVERT: B 138 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8076 (tm-30) REVERT: B 142 PHE cc_start: 0.7335 (t80) cc_final: 0.6805 (t80) REVERT: B 248 TYR cc_start: 0.8619 (t80) cc_final: 0.8391 (t80) REVERT: C 113 ASP cc_start: 0.7665 (m-30) cc_final: 0.7236 (p0) REVERT: C 142 PHE cc_start: 0.7472 (t80) cc_final: 0.6849 (t80) REVERT: D 86 ASP cc_start: 0.8564 (t0) cc_final: 0.8225 (t0) REVERT: D 93 MET cc_start: 0.8267 (ttm) cc_final: 0.7967 (ttp) REVERT: D 142 PHE cc_start: 0.7446 (t80) cc_final: 0.6906 (t80) REVERT: E 113 ASP cc_start: 0.7995 (m-30) cc_final: 0.7662 (p0) REVERT: E 138 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8032 (tm-30) REVERT: E 142 PHE cc_start: 0.7348 (t80) cc_final: 0.6898 (t80) REVERT: E 185 GLN cc_start: 0.7958 (tp-100) cc_final: 0.7552 (tp-100) outliers start: 3 outliers final: 1 residues processed: 129 average time/residue: 0.1154 time to fit residues: 21.8995 Evaluate side-chains 99 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 96 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain E residue 138 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 7.9990 chunk 142 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 150 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 251 ASN B 89 ASN ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 ASN C 89 ASN D 89 ASN D 138 GLN D 285 HIS E 89 ASN ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 GLN E 251 ASN E 285 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.160266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.126475 restraints weight = 14625.959| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.22 r_work: 0.3593 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13015 Z= 0.216 Angle : 0.636 7.141 17735 Z= 0.325 Chirality : 0.048 0.157 1975 Planarity : 0.004 0.049 2260 Dihedral : 5.328 58.547 1716 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.72 % Allowed : 8.63 % Favored : 90.65 % 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: -0.47 (0.23), residues: 1545 helix: 0.84 (0.23), residues: 535 sheet: 0.33 (0.27), residues: 490 loop : -2.17 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 91 TYR 0.017 0.002 TYR A 248 PHE 0.021 0.002 PHE D 247 TRP 0.017 0.001 TRP D 224 HIS 0.004 0.001 HIS E 285 Details of bonding type rmsd covalent geometry : bond 0.00539 (13015) covalent geometry : angle 0.63634 (17735) hydrogen bonds : bond 0.04324 ( 615) hydrogen bonds : angle 4.38453 ( 1905) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.519 Fit side-chains REVERT: A 285 HIS cc_start: 0.6832 (t70) cc_final: 0.6391 (t-90) REVERT: B 113 ASP cc_start: 0.7799 (m-30) cc_final: 0.7326 (p0) REVERT: B 138 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8319 (tm-30) REVERT: B 142 PHE cc_start: 0.7364 (t80) cc_final: 0.6871 (t80) REVERT: C 142 PHE cc_start: 0.7507 (t80) cc_final: 0.6804 (t80) REVERT: C 285 HIS cc_start: 0.6783 (t70) cc_final: 0.6425 (t-90) REVERT: D 86 ASP cc_start: 0.8703 (t0) cc_final: 0.8324 (t0) REVERT: D 142 PHE cc_start: 0.7518 (t80) cc_final: 0.7017 (t80) REVERT: E 138 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8370 (tm-30) outliers start: 10 outliers final: 5 residues processed: 108 average time/residue: 0.1274 time to fit residues: 19.8469 Evaluate side-chains 93 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 113 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 110 optimal weight: 0.0370 chunk 57 optimal weight: 0.5980 chunk 147 optimal weight: 0.7980 overall best weight: 1.0460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.165462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.131764 restraints weight = 14508.065| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.22 r_work: 0.3642 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13015 Z= 0.130 Angle : 0.572 6.653 17735 Z= 0.293 Chirality : 0.046 0.149 1975 Planarity : 0.004 0.047 2260 Dihedral : 5.039 59.203 1716 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.08 % Allowed : 9.57 % Favored : 89.35 % 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: -0.22 (0.23), residues: 1545 helix: 1.10 (0.23), residues: 535 sheet: 0.49 (0.26), residues: 490 loop : -2.13 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 286 TYR 0.015 0.001 TYR C 248 PHE 0.021 0.001 PHE B 247 TRP 0.007 0.001 TRP A 43 HIS 0.004 0.001 HIS E 285 Details of bonding type rmsd covalent geometry : bond 0.00313 (13015) covalent geometry : angle 0.57207 (17735) hydrogen bonds : bond 0.03575 ( 615) hydrogen bonds : angle 4.02916 ( 1905) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 285 HIS cc_start: 0.6864 (t70) cc_final: 0.6450 (t-90) REVERT: B 113 ASP cc_start: 0.7770 (m-30) cc_final: 0.7333 (p0) REVERT: B 138 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8052 (tm-30) REVERT: B 142 PHE cc_start: 0.7309 (t80) cc_final: 0.6795 (t80) REVERT: C 158 ASP cc_start: 0.8251 (m-30) cc_final: 0.7959 (m-30) REVERT: C 285 HIS cc_start: 0.6754 (t70) cc_final: 0.6512 (t-90) REVERT: D 86 ASP cc_start: 0.8668 (t0) cc_final: 0.8291 (t0) REVERT: D 93 MET cc_start: 0.8263 (ttm) cc_final: 0.7929 (ttp) REVERT: D 142 PHE cc_start: 0.7417 (t80) cc_final: 0.6884 (t80) REVERT: E 138 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8238 (tm-30) REVERT: E 185 GLN cc_start: 0.7938 (tp-100) cc_final: 0.7453 (tp-100) outliers start: 15 outliers final: 10 residues processed: 129 average time/residue: 0.1183 time to fit residues: 22.3669 Evaluate side-chains 100 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 149 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 126 optimal weight: 0.0670 chunk 15 optimal weight: 7.9990 chunk 150 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN D 138 GLN ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.165505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.131855 restraints weight = 14472.233| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.23 r_work: 0.3644 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 13015 Z= 0.134 Angle : 0.565 6.515 17735 Z= 0.290 Chirality : 0.045 0.147 1975 Planarity : 0.004 0.044 2260 Dihedral : 4.915 59.761 1716 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.51 % Allowed : 11.01 % Favored : 87.48 % 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: -0.06 (0.23), residues: 1545 helix: 1.25 (0.23), residues: 530 sheet: 0.61 (0.26), residues: 490 loop : -2.07 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 91 TYR 0.014 0.001 TYR C 248 PHE 0.018 0.001 PHE B 247 TRP 0.009 0.001 TRP D 224 HIS 0.004 0.001 HIS E 285 Details of bonding type rmsd covalent geometry : bond 0.00328 (13015) covalent geometry : angle 0.56514 (17735) hydrogen bonds : bond 0.03419 ( 615) hydrogen bonds : angle 3.92475 ( 1905) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.503 Fit side-chains REVERT: A 285 HIS cc_start: 0.6941 (t70) cc_final: 0.6642 (t-90) REVERT: B 113 ASP cc_start: 0.7729 (m-30) cc_final: 0.7356 (p0) REVERT: B 138 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8221 (tm-30) REVERT: B 142 PHE cc_start: 0.7259 (t80) cc_final: 0.6747 (t80) REVERT: D 86 ASP cc_start: 0.8720 (t0) cc_final: 0.8311 (t0) REVERT: D 93 MET cc_start: 0.8268 (ttm) cc_final: 0.7932 (ttp) REVERT: E 138 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8295 (tm-30) outliers start: 21 outliers final: 18 residues processed: 115 average time/residue: 0.1237 time to fit residues: 20.8161 Evaluate side-chains 109 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 83 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 30 optimal weight: 0.0010 chunk 15 optimal weight: 7.9990 chunk 99 optimal weight: 0.5980 chunk 79 optimal weight: 0.4980 chunk 121 optimal weight: 20.0000 chunk 71 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.167921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.134282 restraints weight = 14380.817| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.22 r_work: 0.3673 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13015 Z= 0.112 Angle : 0.548 7.169 17735 Z= 0.280 Chirality : 0.044 0.141 1975 Planarity : 0.004 0.043 2260 Dihedral : 4.771 58.764 1716 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.51 % Allowed : 11.73 % Favored : 86.76 % 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: 0.21 (0.23), residues: 1545 helix: 1.39 (0.23), residues: 535 sheet: 0.94 (0.26), residues: 480 loop : -2.01 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 286 TYR 0.023 0.001 TYR C 248 PHE 0.017 0.001 PHE E 247 TRP 0.006 0.001 TRP D 43 HIS 0.003 0.001 HIS C 285 Details of bonding type rmsd covalent geometry : bond 0.00263 (13015) covalent geometry : angle 0.54783 (17735) hydrogen bonds : bond 0.03131 ( 615) hydrogen bonds : angle 3.75737 ( 1905) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.431 Fit side-chains REVERT: A 285 HIS cc_start: 0.6866 (t70) cc_final: 0.6625 (t-90) REVERT: B 113 ASP cc_start: 0.7629 (m-30) cc_final: 0.7359 (p0) REVERT: B 138 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8031 (tm-30) REVERT: B 142 PHE cc_start: 0.7356 (t80) cc_final: 0.6833 (t80) REVERT: D 86 ASP cc_start: 0.8683 (t0) cc_final: 0.8289 (t0) REVERT: D 93 MET cc_start: 0.8209 (ttm) cc_final: 0.7893 (ttp) REVERT: D 138 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7964 (tm-30) REVERT: E 138 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8152 (tm-30) REVERT: E 185 GLN cc_start: 0.7933 (tp-100) cc_final: 0.7467 (tp-100) outliers start: 21 outliers final: 17 residues processed: 129 average time/residue: 0.1193 time to fit residues: 22.6060 Evaluate side-chains 115 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 129 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 99 optimal weight: 0.0470 chunk 126 optimal weight: 0.0020 chunk 14 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 overall best weight: 0.5688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 ASN ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.176746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.145648 restraints weight = 13990.115| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.06 r_work: 0.3705 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 13015 Z= 0.107 Angle : 0.534 6.257 17735 Z= 0.273 Chirality : 0.044 0.138 1975 Planarity : 0.003 0.042 2260 Dihedral : 4.642 59.741 1716 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.58 % Allowed : 12.09 % Favored : 86.33 % 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: 0.41 (0.23), residues: 1545 helix: 1.55 (0.23), residues: 535 sheet: 1.09 (0.26), residues: 480 loop : -1.94 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 91 TYR 0.018 0.001 TYR C 248 PHE 0.014 0.001 PHE B 247 TRP 0.009 0.001 TRP E 161 HIS 0.004 0.000 HIS E 285 Details of bonding type rmsd covalent geometry : bond 0.00252 (13015) covalent geometry : angle 0.53440 (17735) hydrogen bonds : bond 0.02911 ( 615) hydrogen bonds : angle 3.64334 ( 1905) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.434 Fit side-chains REVERT: B 113 ASP cc_start: 0.7610 (m-30) cc_final: 0.7305 (p0) REVERT: B 138 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8046 (tm-30) REVERT: B 142 PHE cc_start: 0.7282 (t80) cc_final: 0.6755 (t80) REVERT: D 86 ASP cc_start: 0.8689 (t0) cc_final: 0.8291 (t0) REVERT: D 93 MET cc_start: 0.8226 (ttm) cc_final: 0.7930 (ttp) REVERT: D 138 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7857 (tm-30) REVERT: E 138 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8153 (tm-30) REVERT: E 224 TRP cc_start: 0.7484 (m100) cc_final: 0.7256 (m100) outliers start: 22 outliers final: 17 residues processed: 125 average time/residue: 0.1091 time to fit residues: 20.0498 Evaluate side-chains 117 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 138 GLN Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 112 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.177927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.146123 restraints weight = 14422.681| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.14 r_work: 0.3658 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 13015 Z= 0.131 Angle : 0.553 6.471 17735 Z= 0.284 Chirality : 0.045 0.141 1975 Planarity : 0.004 0.041 2260 Dihedral : 4.725 59.178 1716 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.58 % Allowed : 12.81 % Favored : 85.61 % 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: 0.44 (0.23), residues: 1545 helix: 1.55 (0.23), residues: 535 sheet: 1.15 (0.26), residues: 480 loop : -1.95 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 91 TYR 0.022 0.001 TYR C 248 PHE 0.014 0.001 PHE D 247 TRP 0.009 0.001 TRP E 161 HIS 0.006 0.001 HIS C 285 Details of bonding type rmsd covalent geometry : bond 0.00316 (13015) covalent geometry : angle 0.55297 (17735) hydrogen bonds : bond 0.03199 ( 615) hydrogen bonds : angle 3.73005 ( 1905) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.475 Fit side-chains REVERT: B 113 ASP cc_start: 0.7653 (m-30) cc_final: 0.7331 (p0) REVERT: B 138 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8189 (tm-30) REVERT: B 142 PHE cc_start: 0.7378 (t80) cc_final: 0.6857 (t80) REVERT: D 86 ASP cc_start: 0.8717 (t0) cc_final: 0.8304 (t0) REVERT: D 93 MET cc_start: 0.8239 (ttm) cc_final: 0.7911 (ttp) REVERT: E 138 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8361 (tm-30) outliers start: 22 outliers final: 19 residues processed: 121 average time/residue: 0.1143 time to fit residues: 20.3244 Evaluate side-chains 116 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 123 optimal weight: 30.0000 chunk 85 optimal weight: 0.9980 chunk 104 optimal weight: 0.3980 chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.177946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.145883 restraints weight = 14495.830| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.17 r_work: 0.3662 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13015 Z= 0.122 Angle : 0.543 6.257 17735 Z= 0.277 Chirality : 0.045 0.142 1975 Planarity : 0.003 0.042 2260 Dihedral : 4.666 59.004 1716 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.58 % Allowed : 12.95 % Favored : 85.47 % 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: 0.49 (0.23), residues: 1545 helix: 1.64 (0.23), residues: 535 sheet: 1.17 (0.26), residues: 480 loop : -1.96 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 91 TYR 0.021 0.001 TYR C 248 PHE 0.015 0.001 PHE D 247 TRP 0.007 0.001 TRP E 161 HIS 0.004 0.001 HIS C 285 Details of bonding type rmsd covalent geometry : bond 0.00294 (13015) covalent geometry : angle 0.54292 (17735) hydrogen bonds : bond 0.03139 ( 615) hydrogen bonds : angle 3.71120 ( 1905) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.471 Fit side-chains REVERT: B 113 ASP cc_start: 0.7630 (m-30) cc_final: 0.7295 (p0) REVERT: B 138 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8171 (tm-30) REVERT: B 142 PHE cc_start: 0.7358 (t80) cc_final: 0.6772 (t80) REVERT: D 86 ASP cc_start: 0.8716 (t0) cc_final: 0.8295 (t0) REVERT: D 93 MET cc_start: 0.8252 (ttm) cc_final: 0.7925 (ttp) REVERT: E 138 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8340 (tm-30) REVERT: E 196 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7980 (m-30) outliers start: 22 outliers final: 18 residues processed: 117 average time/residue: 0.1197 time to fit residues: 20.5803 Evaluate side-chains 118 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 146 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 GLN ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 200 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.163742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.129390 restraints weight = 14531.578| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.25 r_work: 0.3618 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13015 Z= 0.182 Angle : 0.587 6.373 17735 Z= 0.301 Chirality : 0.047 0.152 1975 Planarity : 0.004 0.041 2260 Dihedral : 4.899 58.296 1716 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.51 % Allowed : 13.31 % Favored : 85.18 % 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: 0.31 (0.23), residues: 1545 helix: 1.45 (0.22), residues: 535 sheet: 1.08 (0.26), residues: 480 loop : -2.01 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 91 TYR 0.018 0.001 TYR C 248 PHE 0.015 0.002 PHE D 247 TRP 0.007 0.001 TRP E 161 HIS 0.003 0.001 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00453 (13015) covalent geometry : angle 0.58711 (17735) hydrogen bonds : bond 0.03730 ( 615) hydrogen bonds : angle 3.94209 ( 1905) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.469 Fit side-chains REVERT: B 113 ASP cc_start: 0.7617 (m-30) cc_final: 0.7349 (p0) REVERT: B 138 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8429 (tm-30) REVERT: D 86 ASP cc_start: 0.8764 (t0) cc_final: 0.8559 (t0) REVERT: D 93 MET cc_start: 0.8364 (ttm) cc_final: 0.8009 (ttp) REVERT: E 138 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8469 (tm-30) REVERT: E 196 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7938 (m-30) outliers start: 21 outliers final: 17 residues processed: 114 average time/residue: 0.1196 time to fit residues: 19.8357 Evaluate side-chains 112 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 138 GLN Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 41 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.178131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.146170 restraints weight = 14501.185| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.17 r_work: 0.3660 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13015 Z= 0.114 Angle : 0.540 6.292 17735 Z= 0.276 Chirality : 0.044 0.143 1975 Planarity : 0.003 0.042 2260 Dihedral : 4.647 58.120 1716 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.44 % Allowed : 13.38 % Favored : 85.18 % 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: 0.52 (0.23), residues: 1545 helix: 1.67 (0.23), residues: 535 sheet: 1.19 (0.26), residues: 480 loop : -1.97 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 91 TYR 0.022 0.001 TYR C 248 PHE 0.016 0.001 PHE D 247 TRP 0.007 0.001 TRP E 161 HIS 0.005 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00269 (13015) covalent geometry : angle 0.53993 (17735) hydrogen bonds : bond 0.03132 ( 615) hydrogen bonds : angle 3.72535 ( 1905) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2182.48 seconds wall clock time: 38 minutes 17.08 seconds (2297.08 seconds total)