Starting phenix.real_space_refine on Wed Mar 4 10:05:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d65_27217/03_2026/8d65_27217.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d65_27217/03_2026/8d65_27217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d65_27217/03_2026/8d65_27217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d65_27217/03_2026/8d65_27217.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d65_27217/03_2026/8d65_27217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d65_27217/03_2026/8d65_27217.map" } resolution = 3.47 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= 0.000 sd= 0.009 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 5 5.49 5 S 30 5.16 5 C 8365 2.51 5 N 2080 2.21 5 O 2300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 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: 12780 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "B" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "C" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "D" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "E" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.96, per 1000 atoms: 0.23 Number of scatterers: 12780 At special positions: 0 Unit cell: (91.3, 91.3, 123.2, 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 30 16.00 P 5 15.00 O 2300 8.00 N 2080 7.00 C 8365 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 568.8 milliseconds 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 15 sheets defined 33.6% alpha, 35.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 62 through 68 removed outlier: 3.707A pdb=" N ASN A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 180 removed outlier: 4.172A pdb=" N SER A 180 " --> pdb=" O HIS A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 207 Processing helix chain 'A' and resid 208 through 220 removed outlier: 3.763A pdb=" N LEU A 212 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 252 removed outlier: 3.634A pdb=" N ILE A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 285 removed outlier: 3.715A pdb=" N ILE A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 removed outlier: 3.542A pdb=" N CYS A 300 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'B' and resid 62 through 68 removed outlier: 3.708A pdb=" N ASN B 68 " --> pdb=" O GLU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 removed outlier: 4.172A pdb=" N SER B 180 " --> pdb=" O HIS B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 207 Processing helix chain 'B' and resid 208 through 220 removed outlier: 3.763A pdb=" N LEU B 212 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 252 removed outlier: 3.633A pdb=" N ILE B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 285 removed outlier: 3.716A pdb=" N ILE B 267 " --> pdb=" O ASP B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 300 removed outlier: 3.542A pdb=" N CYS B 300 " --> pdb=" O ILE B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 317 Processing helix chain 'C' and resid 62 through 68 removed outlier: 3.707A pdb=" N ASN C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 180 removed outlier: 4.172A pdb=" N SER C 180 " --> pdb=" O HIS C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 207 Processing helix chain 'C' and resid 208 through 220 removed outlier: 3.763A pdb=" N LEU C 212 " --> pdb=" O PHE C 208 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP C 220 " --> pdb=" O ILE C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 252 removed outlier: 3.634A pdb=" N ILE C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 285 removed outlier: 3.716A pdb=" N ILE C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 300 removed outlier: 3.542A pdb=" N CYS C 300 " --> pdb=" O ILE C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 317 Processing helix chain 'D' and resid 62 through 68 removed outlier: 3.707A pdb=" N ASN D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 180 removed outlier: 4.173A pdb=" N SER D 180 " --> pdb=" O HIS D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 207 Processing helix chain 'D' and resid 208 through 220 removed outlier: 3.763A pdb=" N LEU D 212 " --> pdb=" O PHE D 208 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP D 220 " --> pdb=" O ILE D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 252 removed outlier: 3.633A pdb=" N ILE D 252 " --> pdb=" O TYR D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 285 removed outlier: 3.716A pdb=" N ILE D 267 " --> pdb=" O ASP D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 300 removed outlier: 3.543A pdb=" N CYS D 300 " --> pdb=" O ILE D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 317 Processing helix chain 'E' and resid 62 through 68 removed outlier: 3.707A pdb=" N ASN E 68 " --> pdb=" O GLU E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 180 removed outlier: 4.172A pdb=" N SER E 180 " --> pdb=" O HIS E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 207 Processing helix chain 'E' and resid 208 through 220 removed outlier: 3.763A pdb=" N LEU E 212 " --> pdb=" O PHE E 208 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP E 220 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 252 removed outlier: 3.634A pdb=" N ILE E 252 " --> pdb=" O TYR E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 285 removed outlier: 3.716A pdb=" N ILE E 267 " --> pdb=" O ASP E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 300 removed outlier: 3.542A pdb=" N CYS E 300 " --> pdb=" O ILE E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 317 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 59 removed outlier: 6.353A pdb=" N THR A 32 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLY A 25 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N THR A 44 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASP A 13 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL A 12 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER A 143 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL A 14 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE A 145 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL A 16 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL A 147 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE A 18 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.801A 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: 6.801A 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 59 removed outlier: 6.353A pdb=" N THR B 32 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY B 25 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N THR B 44 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASP B 13 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL B 12 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER B 143 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL B 14 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE B 145 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N VAL B 16 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL B 147 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE B 18 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.800A 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: 6.800A 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 59 removed outlier: 6.352A pdb=" N THR C 32 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLY C 25 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N THR C 44 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASP C 13 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL C 12 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER C 143 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL C 14 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE C 145 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N VAL C 16 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL C 147 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE C 18 " --> pdb=" O VAL C 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.801A 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: 6.801A 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 59 removed outlier: 6.352A pdb=" N THR D 32 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLY D 25 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LYS D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE D 23 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASP D 36 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N THR D 44 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASP D 13 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL D 12 " --> pdb=" O ARG D 141 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER D 143 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL D 14 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE D 145 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL D 16 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL D 147 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE D 18 " --> pdb=" O VAL D 147 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.801A 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: 6.801A 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 59 removed outlier: 6.353A pdb=" N THR E 32 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLY E 25 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N THR E 44 " --> pdb=" O ASP E 13 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASP E 13 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL E 12 " --> pdb=" O ARG E 141 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER E 143 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL E 14 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE E 145 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL E 16 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL E 147 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE E 18 " --> pdb=" O VAL E 147 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.801A 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: 6.801A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) 615 hydrogen bonds defined for protein. 1770 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: 2.35 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3250 1.33 - 1.45: 2673 1.45 - 1.57: 7132 1.57 - 1.69: 10 1.69 - 1.81: 50 Bond restraints: 13115 Sorted by residual: bond pdb=" C19 PGW D 401 " pdb=" O03 PGW D 401 " ideal model delta sigma weight residual 1.332 1.454 -0.122 2.00e-02 2.50e+03 3.73e+01 bond pdb=" C1 PGW C 401 " pdb=" O01 PGW C 401 " ideal model delta sigma weight residual 1.332 1.454 -0.122 2.00e-02 2.50e+03 3.73e+01 bond pdb=" C19 PGW C 401 " pdb=" O03 PGW C 401 " ideal model delta sigma weight residual 1.332 1.454 -0.122 2.00e-02 2.50e+03 3.73e+01 bond pdb=" C1 PGW D 401 " pdb=" O01 PGW D 401 " ideal model delta sigma weight residual 1.332 1.454 -0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" C19 PGW A 401 " pdb=" O03 PGW A 401 " ideal model delta sigma weight residual 1.332 1.454 -0.122 2.00e-02 2.50e+03 3.71e+01 ... (remaining 13110 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 16707 1.86 - 3.72: 902 3.72 - 5.58: 136 5.58 - 7.45: 35 7.45 - 9.31: 35 Bond angle restraints: 17815 Sorted by residual: angle pdb=" N ILE A 152 " pdb=" CA ILE A 152 " pdb=" C ILE A 152 " ideal model delta sigma weight residual 108.12 117.33 -9.21 1.34e+00 5.57e-01 4.73e+01 angle pdb=" N ILE D 152 " pdb=" CA ILE D 152 " pdb=" C ILE D 152 " ideal model delta sigma weight residual 108.12 117.31 -9.19 1.34e+00 5.57e-01 4.70e+01 angle pdb=" N ILE E 152 " pdb=" CA ILE E 152 " pdb=" C ILE E 152 " ideal model delta sigma weight residual 108.12 117.30 -9.18 1.34e+00 5.57e-01 4.69e+01 angle pdb=" N ILE B 152 " pdb=" CA ILE B 152 " pdb=" C ILE B 152 " ideal model delta sigma weight residual 108.12 117.29 -9.17 1.34e+00 5.57e-01 4.68e+01 angle pdb=" N ILE C 152 " pdb=" CA ILE C 152 " pdb=" C ILE C 152 " ideal model delta sigma weight residual 108.12 117.28 -9.16 1.34e+00 5.57e-01 4.67e+01 ... (remaining 17810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.04: 7290 24.04 - 48.08: 365 48.08 - 72.13: 80 72.13 - 96.17: 15 96.17 - 120.21: 10 Dihedral angle restraints: 7760 sinusoidal: 3255 harmonic: 4505 Sorted by residual: dihedral pdb=" CA LEU C 118 " pdb=" C LEU C 118 " pdb=" N PHE C 119 " pdb=" CA PHE C 119 " ideal model delta harmonic sigma weight residual -180.00 -156.43 -23.57 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA LEU D 118 " pdb=" C LEU D 118 " pdb=" N PHE D 119 " pdb=" CA PHE D 119 " ideal model delta harmonic sigma weight residual 180.00 -156.43 -23.57 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA LEU A 118 " pdb=" C LEU A 118 " pdb=" N PHE A 119 " pdb=" CA PHE A 119 " ideal model delta harmonic sigma weight residual -180.00 -156.46 -23.54 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 7757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1325 0.059 - 0.118: 481 0.118 - 0.177: 95 0.177 - 0.235: 38 0.235 - 0.294: 21 Chirality restraints: 1960 Sorted by residual: chirality pdb=" CA ASP A 153 " pdb=" N ASP A 153 " pdb=" C ASP A 153 " pdb=" CB ASP A 153 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA ASP D 153 " pdb=" N ASP D 153 " pdb=" C ASP D 153 " pdb=" CB ASP D 153 " 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 ASP B 153 " pdb=" N ASP B 153 " pdb=" C ASP B 153 " pdb=" CB ASP B 153 " 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 1957 not shown) Planarity restraints: 2250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 50 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.19e+00 pdb=" N PRO B 51 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 51 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 51 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 50 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO E 51 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO E 51 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 51 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 50 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO A 51 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 51 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 51 " -0.028 5.00e-02 4.00e+02 ... (remaining 2247 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 38 2.48 - 3.08: 8303 3.08 - 3.69: 17523 3.69 - 4.29: 26227 4.29 - 4.90: 46758 Nonbonded interactions: 98849 Sorted by model distance: nonbonded pdb=" CZ PHE A 247 " pdb=" CE2 PHE B 247 " model vdw 1.871 3.640 nonbonded pdb=" CE1 PHE A 247 " pdb=" CE2 PHE B 247 " model vdw 1.965 3.640 nonbonded pdb=" CZ PHE D 247 " pdb=" CE2 PHE E 247 " model vdw 1.978 3.640 nonbonded pdb=" CE1 PHE D 247 " pdb=" CE2 PHE E 247 " model vdw 2.138 3.640 nonbonded pdb=" CE1 PHE B 247 " pdb=" CE2 PHE C 247 " model vdw 2.160 3.640 ... (remaining 98844 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: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.940 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 : 0.010 0.122 13115 Z= 0.495 Angle : 1.028 9.308 17815 Z= 0.610 Chirality : 0.069 0.294 1960 Planarity : 0.005 0.051 2250 Dihedral : 15.837 120.209 4850 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % 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: -3.22 (0.19), residues: 1525 helix: -2.12 (0.18), residues: 530 sheet: -1.23 (0.24), residues: 505 loop : -2.83 (0.24), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 117 TYR 0.009 0.002 TYR B 245 PHE 0.017 0.003 PHE E 304 TRP 0.008 0.002 TRP B 206 HIS 0.004 0.001 HIS C 284 Details of bonding type rmsd covalent geometry : bond 0.00962 (13115) covalent geometry : angle 1.02788 (17815) hydrogen bonds : bond 0.12406 ( 565) hydrogen bonds : angle 6.29238 ( 1770) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.518 Fit side-chains REVERT: A 90 LYS cc_start: 0.9061 (pttt) cc_final: 0.8545 (pttm) REVERT: A 149 THR cc_start: 0.8989 (p) cc_final: 0.8700 (t) REVERT: A 245 TYR cc_start: 0.8935 (t80) cc_final: 0.8203 (t80) REVERT: B 226 GLU cc_start: 0.7405 (mp0) cc_final: 0.6989 (mp0) REVERT: B 252 ILE cc_start: 0.8248 (mm) cc_final: 0.7960 (mm) REVERT: C 38 TYR cc_start: 0.8547 (m-80) cc_final: 0.8332 (m-80) REVERT: C 90 LYS cc_start: 0.9102 (pttt) cc_final: 0.8649 (pttm) REVERT: C 149 THR cc_start: 0.8972 (p) cc_final: 0.8768 (t) REVERT: C 191 ILE cc_start: 0.9100 (mt) cc_final: 0.8889 (mt) REVERT: D 149 THR cc_start: 0.9149 (p) cc_final: 0.8807 (t) REVERT: D 226 GLU cc_start: 0.7654 (mp0) cc_final: 0.7223 (mp0) REVERT: E 86 ASP cc_start: 0.7824 (m-30) cc_final: 0.7492 (m-30) REVERT: E 149 THR cc_start: 0.9099 (p) cc_final: 0.8730 (t) REVERT: E 191 ILE cc_start: 0.9130 (mt) cc_final: 0.8857 (mt) REVERT: E 245 TYR cc_start: 0.8702 (t80) cc_final: 0.8402 (t80) REVERT: E 252 ILE cc_start: 0.8326 (mm) cc_final: 0.8109 (mm) REVERT: E 282 PHE cc_start: 0.8047 (t80) cc_final: 0.7837 (t80) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1213 time to fit residues: 27.5177 Evaluate side-chains 102 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.0870 chunk 91 optimal weight: 0.0040 chunk 149 optimal weight: 2.9990 overall best weight: 0.4570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 184 ASN A 185 GLN A 264 GLN B 177 HIS B 184 ASN B 185 GLN B 264 GLN C 184 ASN C 185 GLN D 184 ASN D 185 GLN E 184 ASN E 185 GLN E 264 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.139547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.105192 restraints weight = 14320.599| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.69 r_work: 0.3143 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13115 Z= 0.096 Angle : 0.479 5.507 17815 Z= 0.254 Chirality : 0.045 0.139 1960 Planarity : 0.004 0.037 2250 Dihedral : 11.621 75.154 1920 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.16 % Allowed : 8.87 % Favored : 89.96 % 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: -1.59 (0.21), residues: 1525 helix: -0.15 (0.22), residues: 520 sheet: -0.58 (0.24), residues: 505 loop : -2.39 (0.23), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 91 TYR 0.012 0.001 TYR B 248 PHE 0.037 0.001 PHE E 247 TRP 0.007 0.001 TRP D 220 HIS 0.001 0.001 HIS E 177 Details of bonding type rmsd covalent geometry : bond 0.00217 (13115) covalent geometry : angle 0.47926 (17815) hydrogen bonds : bond 0.02953 ( 565) hydrogen bonds : angle 4.31723 ( 1770) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.345 Fit side-chains REVERT: A 90 LYS cc_start: 0.9323 (pttt) cc_final: 0.8972 (pttm) REVERT: A 149 THR cc_start: 0.9198 (p) cc_final: 0.8975 (t) REVERT: A 245 TYR cc_start: 0.8998 (t80) cc_final: 0.8227 (t80) REVERT: B 226 GLU cc_start: 0.7786 (mp0) cc_final: 0.7377 (mp0) REVERT: C 90 LYS cc_start: 0.9319 (pttt) cc_final: 0.8956 (pttm) REVERT: C 208 PHE cc_start: 0.9198 (m-80) cc_final: 0.8919 (m-80) REVERT: D 245 TYR cc_start: 0.8936 (t80) cc_final: 0.8374 (t80) REVERT: E 86 ASP cc_start: 0.8414 (m-30) cc_final: 0.8178 (m-30) REVERT: E 149 THR cc_start: 0.9208 (p) cc_final: 0.8905 (t) REVERT: E 282 PHE cc_start: 0.8191 (t80) cc_final: 0.7985 (t80) outliers start: 16 outliers final: 7 residues processed: 131 average time/residue: 0.0761 time to fit residues: 16.0683 Evaluate side-chains 107 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain E residue 64 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 87 optimal weight: 0.0570 chunk 90 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 141 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 58 optimal weight: 0.0070 chunk 17 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN D 264 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.171052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.141243 restraints weight = 13541.506| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.77 r_work: 0.2972 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13115 Z= 0.094 Angle : 0.446 4.999 17815 Z= 0.233 Chirality : 0.044 0.140 1960 Planarity : 0.003 0.033 2250 Dihedral : 10.070 73.006 1920 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.95 % Allowed : 10.91 % Favored : 88.15 % 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: -0.72 (0.22), residues: 1525 helix: 0.60 (0.24), residues: 530 sheet: -0.07 (0.24), residues: 505 loop : -2.06 (0.24), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 105 TYR 0.007 0.001 TYR A 245 PHE 0.027 0.001 PHE B 247 TRP 0.009 0.001 TRP D 220 HIS 0.001 0.000 HIS D 284 Details of bonding type rmsd covalent geometry : bond 0.00219 (13115) covalent geometry : angle 0.44558 (17815) hydrogen bonds : bond 0.02745 ( 565) hydrogen bonds : angle 3.83516 ( 1770) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.320 Fit side-chains REVERT: A 90 LYS cc_start: 0.9250 (pttt) cc_final: 0.8894 (pttm) REVERT: A 149 THR cc_start: 0.9222 (p) cc_final: 0.9009 (t) REVERT: A 245 TYR cc_start: 0.9033 (t80) cc_final: 0.8194 (t80) REVERT: B 226 GLU cc_start: 0.7721 (mp0) cc_final: 0.7344 (mp0) REVERT: C 208 PHE cc_start: 0.9134 (m-80) cc_final: 0.8905 (m-80) REVERT: C 265 MET cc_start: 0.7911 (mtt) cc_final: 0.7688 (mtp) REVERT: D 245 TYR cc_start: 0.8866 (t80) cc_final: 0.8185 (t80) REVERT: D 247 PHE cc_start: 0.8612 (t80) cc_final: 0.8401 (t80) REVERT: D 265 MET cc_start: 0.8163 (mtt) cc_final: 0.7865 (mtp) REVERT: E 86 ASP cc_start: 0.8334 (m-30) cc_final: 0.8023 (m-30) outliers start: 13 outliers final: 6 residues processed: 124 average time/residue: 0.0773 time to fit residues: 15.9736 Evaluate side-chains 110 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 104 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain E residue 134 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 74 optimal weight: 9.9990 chunk 54 optimal weight: 0.0030 chunk 34 optimal weight: 0.9980 chunk 104 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 118 optimal weight: 30.0000 chunk 27 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 overall best weight: 2.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.134391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.103675 restraints weight = 14430.195| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.52 r_work: 0.3122 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13115 Z= 0.166 Angle : 0.496 5.216 17815 Z= 0.260 Chirality : 0.047 0.147 1960 Planarity : 0.004 0.029 2250 Dihedral : 9.982 74.332 1920 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.31 % Allowed : 11.42 % Favored : 87.27 % 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: -0.42 (0.22), residues: 1525 helix: 1.00 (0.24), residues: 530 sheet: 0.06 (0.25), residues: 505 loop : -2.03 (0.24), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 255 TYR 0.009 0.001 TYR B 270 PHE 0.027 0.002 PHE D 247 TRP 0.014 0.001 TRP D 220 HIS 0.003 0.001 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00411 (13115) covalent geometry : angle 0.49611 (17815) hydrogen bonds : bond 0.03176 ( 565) hydrogen bonds : angle 3.80934 ( 1770) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.485 Fit side-chains REVERT: A 90 LYS cc_start: 0.9291 (pttt) cc_final: 0.8912 (pttm) REVERT: A 245 TYR cc_start: 0.9090 (t80) cc_final: 0.8263 (t80) REVERT: B 226 GLU cc_start: 0.7734 (mp0) cc_final: 0.7339 (mp0) REVERT: D 94 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8635 (mt) REVERT: D 245 TYR cc_start: 0.8921 (t80) cc_final: 0.8355 (t80) REVERT: E 86 ASP cc_start: 0.8311 (m-30) cc_final: 0.8014 (m-30) outliers start: 18 outliers final: 12 residues processed: 121 average time/residue: 0.0811 time to fit residues: 16.3573 Evaluate side-chains 109 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 189 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.136726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.106431 restraints weight = 14300.287| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.56 r_work: 0.3152 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13115 Z= 0.106 Angle : 0.440 4.892 17815 Z= 0.230 Chirality : 0.045 0.136 1960 Planarity : 0.003 0.027 2250 Dihedral : 9.467 70.634 1920 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.16 % Allowed : 12.44 % Favored : 86.40 % 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: -0.01 (0.23), residues: 1525 helix: 1.33 (0.24), residues: 530 sheet: 0.32 (0.25), residues: 505 loop : -1.86 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 255 TYR 0.007 0.001 TYR C 248 PHE 0.030 0.001 PHE D 247 TRP 0.012 0.001 TRP D 220 HIS 0.002 0.000 HIS D 284 Details of bonding type rmsd covalent geometry : bond 0.00257 (13115) covalent geometry : angle 0.44032 (17815) hydrogen bonds : bond 0.02744 ( 565) hydrogen bonds : angle 3.58636 ( 1770) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.457 Fit side-chains REVERT: A 90 LYS cc_start: 0.9259 (pttt) cc_final: 0.8908 (pttm) REVERT: A 245 TYR cc_start: 0.9032 (t80) cc_final: 0.8081 (t80) REVERT: B 226 GLU cc_start: 0.7798 (mp0) cc_final: 0.7380 (mp0) REVERT: C 265 MET cc_start: 0.7973 (mtt) cc_final: 0.7750 (mtp) REVERT: D 94 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8604 (mt) REVERT: D 245 TYR cc_start: 0.8882 (t80) cc_final: 0.8329 (t80) REVERT: E 86 ASP cc_start: 0.8479 (m-30) cc_final: 0.8182 (m-30) outliers start: 16 outliers final: 11 residues processed: 123 average time/residue: 0.0781 time to fit residues: 16.0988 Evaluate side-chains 111 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 134 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 9 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 27 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 71 optimal weight: 0.0030 chunk 11 optimal weight: 2.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.136792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.106655 restraints weight = 14198.545| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.54 r_work: 0.3184 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13115 Z= 0.109 Angle : 0.442 4.875 17815 Z= 0.230 Chirality : 0.045 0.137 1960 Planarity : 0.003 0.027 2250 Dihedral : 9.254 69.944 1920 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.31 % Allowed : 13.53 % Favored : 85.16 % 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: 0.25 (0.23), residues: 1525 helix: 1.56 (0.24), residues: 530 sheet: 0.50 (0.25), residues: 505 loop : -1.77 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 255 TYR 0.008 0.001 TYR C 248 PHE 0.031 0.002 PHE D 247 TRP 0.016 0.001 TRP D 220 HIS 0.002 0.000 HIS E 284 Details of bonding type rmsd covalent geometry : bond 0.00263 (13115) covalent geometry : angle 0.44187 (17815) hydrogen bonds : bond 0.02763 ( 565) hydrogen bonds : angle 3.50492 ( 1770) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.369 Fit side-chains REVERT: A 90 LYS cc_start: 0.9289 (pttt) cc_final: 0.8921 (pttm) REVERT: A 245 TYR cc_start: 0.8973 (t80) cc_final: 0.8055 (t80) REVERT: D 94 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8607 (mt) REVERT: D 245 TYR cc_start: 0.8869 (t80) cc_final: 0.8287 (t80) REVERT: E 86 ASP cc_start: 0.8467 (m-30) cc_final: 0.8181 (m-30) REVERT: E 265 MET cc_start: 0.7939 (mtt) cc_final: 0.7665 (mtp) outliers start: 18 outliers final: 14 residues processed: 121 average time/residue: 0.0768 time to fit residues: 15.6632 Evaluate side-chains 117 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 189 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 87 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 120 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.128583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.098506 restraints weight = 14595.478| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.56 r_work: 0.2975 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.054 13115 Z= 0.359 Angle : 0.638 8.000 17815 Z= 0.335 Chirality : 0.053 0.170 1960 Planarity : 0.004 0.035 2250 Dihedral : 10.474 79.985 1920 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.38 % Allowed : 14.84 % Favored : 83.78 % 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: -0.38 (0.22), residues: 1525 helix: 1.11 (0.23), residues: 530 sheet: -0.08 (0.25), residues: 500 loop : -1.88 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 99 TYR 0.015 0.002 TYR D 38 PHE 0.032 0.003 PHE D 247 TRP 0.022 0.002 TRP D 220 HIS 0.005 0.001 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00913 (13115) covalent geometry : angle 0.63762 (17815) hydrogen bonds : bond 0.04134 ( 565) hydrogen bonds : angle 4.02961 ( 1770) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.449 Fit side-chains REVERT: A 245 TYR cc_start: 0.9201 (t80) cc_final: 0.8291 (t80) REVERT: C 226 GLU cc_start: 0.7866 (mp0) cc_final: 0.7627 (mp0) REVERT: E 86 ASP cc_start: 0.8387 (m-30) cc_final: 0.8125 (m-30) REVERT: E 90 LYS cc_start: 0.9275 (pttt) cc_final: 0.9007 (pttm) REVERT: E 226 GLU cc_start: 0.7619 (mp0) cc_final: 0.7148 (mp0) outliers start: 19 outliers final: 13 residues processed: 120 average time/residue: 0.0873 time to fit residues: 17.0346 Evaluate side-chains 108 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 189 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 53 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 0.0470 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.134479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.104433 restraints weight = 14175.847| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.52 r_work: 0.3085 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13115 Z= 0.113 Angle : 0.464 4.917 17815 Z= 0.244 Chirality : 0.045 0.141 1960 Planarity : 0.003 0.028 2250 Dihedral : 9.598 72.583 1920 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.16 % Allowed : 15.13 % Favored : 83.71 % 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: 0.03 (0.23), residues: 1525 helix: 1.52 (0.24), residues: 530 sheet: 0.02 (0.26), residues: 475 loop : -1.51 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 91 TYR 0.008 0.001 TYR A 270 PHE 0.030 0.002 PHE D 247 TRP 0.017 0.001 TRP D 220 HIS 0.002 0.000 HIS D 284 Details of bonding type rmsd covalent geometry : bond 0.00269 (13115) covalent geometry : angle 0.46394 (17815) hydrogen bonds : bond 0.02919 ( 565) hydrogen bonds : angle 3.67065 ( 1770) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.472 Fit side-chains REVERT: A 90 LYS cc_start: 0.9284 (pttt) cc_final: 0.8916 (pttm) REVERT: A 245 TYR cc_start: 0.9019 (t80) cc_final: 0.7980 (t80) REVERT: C 226 GLU cc_start: 0.7799 (mp0) cc_final: 0.7572 (mp0) REVERT: C 265 MET cc_start: 0.7917 (mtt) cc_final: 0.7683 (mtp) REVERT: D 265 MET cc_start: 0.8030 (mtt) cc_final: 0.7705 (mtp) REVERT: E 86 ASP cc_start: 0.8324 (m-30) cc_final: 0.8022 (m-30) REVERT: E 156 GLU cc_start: 0.7838 (mp0) cc_final: 0.6838 (tm-30) REVERT: E 265 MET cc_start: 0.7914 (mtt) cc_final: 0.7625 (mtp) outliers start: 16 outliers final: 14 residues processed: 125 average time/residue: 0.0814 time to fit residues: 17.0507 Evaluate side-chains 117 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 189 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 0 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 0.2980 chunk 99 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 131 optimal weight: 0.3980 chunk 35 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 139 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.135206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.104787 restraints weight = 14235.116| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.58 r_work: 0.3124 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13115 Z= 0.117 Angle : 0.457 4.876 17815 Z= 0.239 Chirality : 0.045 0.138 1960 Planarity : 0.003 0.028 2250 Dihedral : 9.256 71.112 1920 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.02 % Allowed : 15.42 % Favored : 83.56 % 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: 0.27 (0.23), residues: 1525 helix: 1.77 (0.24), residues: 525 sheet: 0.12 (0.25), residues: 485 loop : -1.43 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 91 TYR 0.010 0.001 TYR B 245 PHE 0.030 0.001 PHE D 247 TRP 0.017 0.001 TRP D 220 HIS 0.002 0.001 HIS D 284 Details of bonding type rmsd covalent geometry : bond 0.00287 (13115) covalent geometry : angle 0.45710 (17815) hydrogen bonds : bond 0.02827 ( 565) hydrogen bonds : angle 3.56065 ( 1770) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.348 Fit side-chains REVERT: A 90 LYS cc_start: 0.9287 (pttt) cc_final: 0.8923 (pttm) REVERT: A 245 TYR cc_start: 0.8998 (t80) cc_final: 0.8068 (t80) REVERT: C 226 GLU cc_start: 0.7807 (mp0) cc_final: 0.7433 (mp0) REVERT: C 265 MET cc_start: 0.7981 (mtt) cc_final: 0.7749 (mtp) REVERT: E 86 ASP cc_start: 0.8379 (m-30) cc_final: 0.8093 (m-30) REVERT: E 156 GLU cc_start: 0.7869 (mp0) cc_final: 0.6857 (tm-30) REVERT: E 265 MET cc_start: 0.7932 (mtt) cc_final: 0.7647 (mtp) outliers start: 14 outliers final: 13 residues processed: 116 average time/residue: 0.0709 time to fit residues: 13.7647 Evaluate side-chains 112 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 189 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 46 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 84 optimal weight: 0.0470 chunk 38 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 72 optimal weight: 0.0970 chunk 49 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 overall best weight: 1.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.165635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.136299 restraints weight = 13757.015| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.58 r_work: 0.3095 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13115 Z= 0.146 Angle : 0.478 5.057 17815 Z= 0.251 Chirality : 0.046 0.144 1960 Planarity : 0.003 0.028 2250 Dihedral : 9.287 72.006 1920 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.09 % Allowed : 15.64 % Favored : 83.27 % 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: 0.30 (0.23), residues: 1525 helix: 1.77 (0.24), residues: 525 sheet: 0.39 (0.25), residues: 515 loop : -1.77 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 194 TYR 0.015 0.001 TYR B 245 PHE 0.028 0.002 PHE D 247 TRP 0.020 0.001 TRP D 220 HIS 0.002 0.001 HIS C 284 Details of bonding type rmsd covalent geometry : bond 0.00364 (13115) covalent geometry : angle 0.47769 (17815) hydrogen bonds : bond 0.03006 ( 565) hydrogen bonds : angle 3.59543 ( 1770) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.471 Fit side-chains REVERT: A 90 LYS cc_start: 0.9317 (pttt) cc_final: 0.8965 (pttm) REVERT: A 245 TYR cc_start: 0.9065 (t80) cc_final: 0.8143 (t80) REVERT: C 114 MET cc_start: 0.8998 (mtp) cc_final: 0.8752 (mtp) REVERT: C 226 GLU cc_start: 0.7872 (mp0) cc_final: 0.7480 (mp0) REVERT: E 86 ASP cc_start: 0.8459 (m-30) cc_final: 0.8184 (m-30) REVERT: E 156 GLU cc_start: 0.7993 (mp0) cc_final: 0.7103 (tm-30) outliers start: 15 outliers final: 13 residues processed: 115 average time/residue: 0.0802 time to fit residues: 15.5345 Evaluate side-chains 113 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 189 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 18 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 chunk 147 optimal weight: 0.8980 chunk 135 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 148 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.137353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.106898 restraints weight = 14129.107| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.58 r_work: 0.2974 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13115 Z= 0.093 Angle : 0.436 4.818 17815 Z= 0.229 Chirality : 0.044 0.133 1960 Planarity : 0.003 0.028 2250 Dihedral : 8.910 68.452 1920 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.95 % Allowed : 15.71 % Favored : 83.35 % 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: 0.54 (0.23), residues: 1525 helix: 1.96 (0.24), residues: 525 sheet: 0.34 (0.25), residues: 485 loop : -1.32 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 194 TYR 0.015 0.001 TYR B 245 PHE 0.023 0.001 PHE D 247 TRP 0.017 0.001 TRP D 220 HIS 0.002 0.000 HIS D 284 Details of bonding type rmsd covalent geometry : bond 0.00218 (13115) covalent geometry : angle 0.43648 (17815) hydrogen bonds : bond 0.02616 ( 565) hydrogen bonds : angle 3.45112 ( 1770) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2524.33 seconds wall clock time: 43 minutes 57.16 seconds (2637.16 seconds total)