Starting phenix.real_space_refine on Mon Dec 30 09:28:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d65_27217/12_2024/8d65_27217.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d65_27217/12_2024/8d65_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d65_27217/12_2024/8d65_27217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d65_27217/12_2024/8d65_27217.map" model { file = "/net/cci-nas-00/data/ceres_data/8d65_27217/12_2024/8d65_27217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d65_27217/12_2024/8d65_27217.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 7.25, per 1000 atoms: 0.57 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: 3.19 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.47 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: 4.00 Time building geometry restraints manager: 3.60 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: 0.00 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: 0.310 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 30.180 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.650 ------------------------------------------------------------------------------- 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= 0.633 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.002 TRP B 206 HIS 0.004 0.001 HIS C 284 PHE 0.017 0.003 PHE E 304 TYR 0.009 0.002 TYR B 245 ARG 0.003 0.000 ARG A 117 *********************** 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 : 1.380 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: 0.2838 time to fit residues: 63.9769 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 : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 87 optimal weight: 0.0970 chunk 136 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN A 185 GLN A 264 GLN B 177 HIS B 184 ASN B 185 GLN B 264 GLN C 177 HIS 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13115 Z= 0.171 Angle : 0.490 5.559 17815 Z= 0.260 Chirality : 0.045 0.138 1960 Planarity : 0.004 0.037 2250 Dihedral : 11.693 75.966 1920 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.16 % Allowed : 9.38 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.21), residues: 1525 helix: -0.18 (0.22), residues: 520 sheet: -0.62 (0.24), residues: 505 loop : -2.43 (0.23), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 220 HIS 0.001 0.001 HIS B 284 PHE 0.035 0.001 PHE E 247 TYR 0.010 0.001 TYR B 258 ARG 0.004 0.000 ARG A 255 *********************** 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 128 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 1.946 Fit side-chains REVERT: A 90 LYS cc_start: 0.9084 (pttt) cc_final: 0.8578 (pttm) REVERT: A 149 THR cc_start: 0.8994 (p) cc_final: 0.8767 (t) REVERT: A 245 TYR cc_start: 0.8850 (t80) cc_final: 0.8016 (t80) REVERT: B 114 MET cc_start: 0.9065 (mtt) cc_final: 0.8853 (mtt) REVERT: B 226 GLU cc_start: 0.7416 (mp0) cc_final: 0.7062 (mp0) REVERT: C 90 LYS cc_start: 0.9081 (pttt) cc_final: 0.8659 (pttm) REVERT: D 245 TYR cc_start: 0.8656 (t80) cc_final: 0.8029 (t80) REVERT: E 86 ASP cc_start: 0.7851 (m-30) cc_final: 0.7538 (m-30) REVERT: E 282 PHE cc_start: 0.8036 (t80) cc_final: 0.7795 (t80) outliers start: 16 outliers final: 7 residues processed: 127 average time/residue: 0.2235 time to fit residues: 45.7233 Evaluate side-chains 105 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 2.096 ------------------------------------------------------------------------------- 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 260 THR Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 134 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13115 Z= 0.317 Angle : 0.528 5.185 17815 Z= 0.278 Chirality : 0.047 0.154 1960 Planarity : 0.004 0.033 2250 Dihedral : 10.598 76.356 1920 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.60 % Allowed : 10.69 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.21), residues: 1525 helix: 0.45 (0.23), residues: 530 sheet: -0.30 (0.24), residues: 505 loop : -2.20 (0.24), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 220 HIS 0.003 0.001 HIS D 284 PHE 0.039 0.002 PHE E 247 TYR 0.009 0.001 TYR B 270 ARG 0.003 0.000 ARG B 255 *********************** 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 128 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 1.557 Fit side-chains REVERT: A 90 LYS cc_start: 0.9049 (pttt) cc_final: 0.8531 (pttm) REVERT: A 245 TYR cc_start: 0.8864 (t80) cc_final: 0.7952 (t80) REVERT: B 226 GLU cc_start: 0.7510 (mp0) cc_final: 0.7195 (mp0) REVERT: C 226 GLU cc_start: 0.7640 (mp0) cc_final: 0.7420 (mp0) REVERT: D 94 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8301 (mt) REVERT: D 236 PHE cc_start: 0.8795 (m-80) cc_final: 0.8574 (m-80) REVERT: D 245 TYR cc_start: 0.8681 (t80) cc_final: 0.8037 (t80) REVERT: E 86 ASP cc_start: 0.7785 (m-30) cc_final: 0.7493 (m-30) REVERT: E 282 PHE cc_start: 0.8062 (t80) cc_final: 0.7848 (t80) outliers start: 22 outliers final: 15 residues processed: 126 average time/residue: 0.2006 time to fit residues: 40.6964 Evaluate side-chains 116 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 1.572 ------------------------------------------------------------------------------- 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 253 LEU 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 C residue 253 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 94 LEU 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 134 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 70 optimal weight: 0.0050 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 overall best weight: 1.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13115 Z= 0.198 Angle : 0.461 4.960 17815 Z= 0.242 Chirality : 0.045 0.141 1960 Planarity : 0.003 0.031 2250 Dihedral : 9.913 73.667 1920 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.67 % Allowed : 11.78 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.22), residues: 1525 helix: 0.98 (0.24), residues: 530 sheet: 0.05 (0.25), residues: 505 loop : -2.03 (0.24), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 220 HIS 0.002 0.001 HIS B 284 PHE 0.034 0.001 PHE E 247 TYR 0.007 0.001 TYR D 38 ARG 0.002 0.000 ARG A 255 *********************** 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 136 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 1.462 Fit side-chains REVERT: A 90 LYS cc_start: 0.9043 (pttt) cc_final: 0.8525 (pttm) REVERT: A 245 TYR cc_start: 0.8774 (t80) cc_final: 0.7817 (t80) REVERT: B 226 GLU cc_start: 0.7524 (mp0) cc_final: 0.7199 (mp0) REVERT: C 226 GLU cc_start: 0.7613 (mp0) cc_final: 0.7296 (mp0) REVERT: D 94 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8293 (mt) REVERT: D 245 TYR cc_start: 0.8592 (t80) cc_final: 0.8010 (t80) REVERT: E 86 ASP cc_start: 0.7736 (m-30) cc_final: 0.7421 (m-30) REVERT: E 282 PHE cc_start: 0.8044 (t80) cc_final: 0.7828 (t80) outliers start: 23 outliers final: 16 residues processed: 133 average time/residue: 0.2032 time to fit residues: 43.9198 Evaluate side-chains 117 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 1.511 ------------------------------------------------------------------------------- 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 253 LEU 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 C residue 253 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 134 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 123 optimal weight: 0.1980 chunk 100 optimal weight: 0.0980 chunk 0 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13115 Z= 0.312 Angle : 0.515 5.360 17815 Z= 0.270 Chirality : 0.048 0.149 1960 Planarity : 0.004 0.030 2250 Dihedral : 9.962 76.502 1920 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.60 % Allowed : 13.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.22), residues: 1525 helix: 1.12 (0.24), residues: 530 sheet: 0.04 (0.25), residues: 505 loop : -2.02 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 220 HIS 0.003 0.001 HIS C 284 PHE 0.020 0.002 PHE C 282 TYR 0.008 0.001 TYR A 248 ARG 0.002 0.000 ARG C 255 *********************** 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 123 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 1.648 Fit side-chains REVERT: A 90 LYS cc_start: 0.9050 (pttt) cc_final: 0.8534 (pttm) REVERT: B 226 GLU cc_start: 0.7584 (mp0) cc_final: 0.7258 (mp0) REVERT: C 226 GLU cc_start: 0.7639 (mp0) cc_final: 0.7401 (mp0) REVERT: D 94 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8314 (mt) REVERT: E 86 ASP cc_start: 0.7812 (m-30) cc_final: 0.7508 (m-30) REVERT: E 282 PHE cc_start: 0.8066 (t80) cc_final: 0.7804 (t80) outliers start: 22 outliers final: 14 residues processed: 120 average time/residue: 0.1926 time to fit residues: 38.0923 Evaluate side-chains 111 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 1.645 ------------------------------------------------------------------------------- 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 253 LEU Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain E residue 64 GLU 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 48 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 145 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2412 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= 0.148 Angle : 0.437 4.863 17815 Z= 0.228 Chirality : 0.045 0.134 1960 Planarity : 0.003 0.029 2250 Dihedral : 9.356 71.157 1920 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.45 % Allowed : 13.67 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.23), residues: 1525 helix: 1.46 (0.24), residues: 530 sheet: 0.05 (0.26), residues: 475 loop : -1.53 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 220 HIS 0.001 0.000 HIS A 284 PHE 0.021 0.001 PHE A 247 TYR 0.006 0.001 TYR E 38 ARG 0.001 0.000 ARG C 91 *********************** 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 132 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 1.467 Fit side-chains REVERT: A 245 TYR cc_start: 0.8682 (t80) cc_final: 0.7640 (t80) REVERT: B 226 GLU cc_start: 0.7544 (mp0) cc_final: 0.7210 (mp0) REVERT: C 226 GLU cc_start: 0.7617 (mp0) cc_final: 0.7307 (mp0) REVERT: D 245 TYR cc_start: 0.8532 (t80) cc_final: 0.7870 (t80) REVERT: E 86 ASP cc_start: 0.7808 (m-30) cc_final: 0.7476 (m-30) REVERT: E 265 MET cc_start: 0.6988 (mtt) cc_final: 0.6747 (mtp) REVERT: E 282 PHE cc_start: 0.8036 (t80) cc_final: 0.7796 (t80) outliers start: 20 outliers final: 14 residues processed: 129 average time/residue: 0.1877 time to fit residues: 40.0733 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 : 1.528 ------------------------------------------------------------------------------- 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 253 LEU Chi-restraints excluded: chain C residue 134 SER 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 D residue 253 LEU Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 134 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 88 optimal weight: 20.0000 chunk 66 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13115 Z= 0.302 Angle : 0.507 5.318 17815 Z= 0.265 Chirality : 0.048 0.149 1960 Planarity : 0.004 0.029 2250 Dihedral : 9.627 75.299 1920 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.53 % Allowed : 14.62 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.23), residues: 1525 helix: 1.44 (0.24), residues: 530 sheet: -0.06 (0.26), residues: 475 loop : -1.57 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 220 HIS 0.003 0.001 HIS B 284 PHE 0.029 0.002 PHE D 247 TYR 0.008 0.001 TYR D 38 ARG 0.002 0.000 ARG D 194 *********************** 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 123 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 1.371 Fit side-chains REVERT: A 90 LYS cc_start: 0.9042 (pttt) cc_final: 0.8509 (pttm) REVERT: B 226 GLU cc_start: 0.7599 (mp0) cc_final: 0.7270 (mp0) REVERT: C 226 GLU cc_start: 0.7609 (mp0) cc_final: 0.7375 (mp0) REVERT: D 94 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8342 (mt) REVERT: E 86 ASP cc_start: 0.7815 (m-30) cc_final: 0.7511 (m-30) REVERT: E 282 PHE cc_start: 0.8030 (t80) cc_final: 0.7759 (t80) outliers start: 21 outliers final: 15 residues processed: 120 average time/residue: 0.2023 time to fit residues: 39.8321 Evaluate side-chains 113 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU 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 C residue 134 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 134 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13115 Z= 0.233 Angle : 0.477 4.946 17815 Z= 0.250 Chirality : 0.046 0.141 1960 Planarity : 0.003 0.028 2250 Dihedral : 9.441 72.801 1920 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.60 % Allowed : 14.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.23), residues: 1525 helix: 1.54 (0.24), residues: 530 sheet: 0.00 (0.25), residues: 475 loop : -1.54 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 220 HIS 0.002 0.001 HIS B 284 PHE 0.028 0.002 PHE D 247 TYR 0.013 0.001 TYR C 245 ARG 0.002 0.000 ARG D 194 *********************** 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 118 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 1.388 Fit side-chains REVERT: A 245 TYR cc_start: 0.8783 (t80) cc_final: 0.7779 (t80) REVERT: B 226 GLU cc_start: 0.7571 (mp0) cc_final: 0.7255 (mp0) REVERT: C 226 GLU cc_start: 0.7627 (mp0) cc_final: 0.7411 (mp0) REVERT: D 94 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8380 (mt) REVERT: E 86 ASP cc_start: 0.7812 (m-30) cc_final: 0.7515 (m-30) REVERT: E 282 PHE cc_start: 0.8002 (t80) cc_final: 0.7737 (t80) outliers start: 22 outliers final: 18 residues processed: 114 average time/residue: 0.1843 time to fit residues: 34.5782 Evaluate side-chains 114 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 1.395 ------------------------------------------------------------------------------- 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 64 GLU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 152 ILE 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 94 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 134 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.0980 chunk 138 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 121 optimal weight: 0.3980 chunk 127 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13115 Z= 0.198 Angle : 0.457 4.918 17815 Z= 0.239 Chirality : 0.046 0.139 1960 Planarity : 0.003 0.028 2250 Dihedral : 9.217 71.826 1920 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.53 % Allowed : 14.55 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.23), residues: 1525 helix: 1.67 (0.24), residues: 530 sheet: 0.17 (0.26), residues: 475 loop : -1.52 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 220 HIS 0.002 0.001 HIS E 284 PHE 0.023 0.002 PHE D 247 TYR 0.012 0.001 TYR C 245 ARG 0.001 0.000 ARG D 194 *********************** 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 117 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 1.457 Fit side-chains REVERT: A 245 TYR cc_start: 0.8701 (t80) cc_final: 0.7732 (t80) REVERT: B 226 GLU cc_start: 0.7767 (mp0) cc_final: 0.7417 (mp0) REVERT: C 226 GLU cc_start: 0.7617 (mp0) cc_final: 0.7311 (mp0) REVERT: D 94 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8370 (mt) REVERT: E 86 ASP cc_start: 0.7805 (m-30) cc_final: 0.7510 (m-30) REVERT: E 265 MET cc_start: 0.7020 (mtt) cc_final: 0.6791 (mtp) REVERT: E 282 PHE cc_start: 0.8007 (t80) cc_final: 0.7738 (t80) outliers start: 21 outliers final: 16 residues processed: 114 average time/residue: 0.1889 time to fit residues: 36.0498 Evaluate side-chains 111 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 1.516 ------------------------------------------------------------------------------- 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 64 GLU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 134 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 chunk 118 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 91 optimal weight: 0.0010 chunk 72 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 36 optimal weight: 0.0980 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13115 Z= 0.140 Angle : 0.435 4.866 17815 Z= 0.227 Chirality : 0.044 0.133 1960 Planarity : 0.003 0.028 2250 Dihedral : 8.914 69.188 1920 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.53 % Allowed : 14.47 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.23), residues: 1525 helix: 1.92 (0.24), residues: 525 sheet: 0.33 (0.25), residues: 485 loop : -1.41 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 220 HIS 0.002 0.000 HIS C 284 PHE 0.021 0.001 PHE D 247 TYR 0.011 0.001 TYR C 245 ARG 0.001 0.000 ARG D 99 ********************** 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 125 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 1.791 Fit side-chains REVERT: A 245 TYR cc_start: 0.8629 (t80) cc_final: 0.7557 (t80) REVERT: C 226 GLU cc_start: 0.7588 (mp0) cc_final: 0.7306 (mp0) REVERT: D 94 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8311 (mt) REVERT: D 245 TYR cc_start: 0.8529 (t80) cc_final: 0.7950 (t80) REVERT: E 86 ASP cc_start: 0.7797 (m-30) cc_final: 0.7498 (m-30) REVERT: E 265 MET cc_start: 0.6994 (mtt) cc_final: 0.6775 (mtp) REVERT: E 282 PHE cc_start: 0.7983 (t80) cc_final: 0.7747 (t80) outliers start: 21 outliers final: 16 residues processed: 121 average time/residue: 0.1870 time to fit residues: 38.0440 Evaluate side-chains 114 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 1.679 ------------------------------------------------------------------------------- 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 64 GLU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 134 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 33 optimal weight: 0.4980 chunk 119 optimal weight: 0.2980 chunk 49 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.3420 r_free = 0.3420 target = 0.135050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.105798 restraints weight = 14143.727| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.44 r_work: 0.2920 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13115 Z= 0.205 Angle : 0.463 4.939 17815 Z= 0.242 Chirality : 0.046 0.141 1960 Planarity : 0.003 0.028 2250 Dihedral : 9.039 71.689 1920 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.23), residues: 1525 helix: 1.94 (0.24), residues: 525 sheet: 0.30 (0.25), residues: 485 loop : -1.42 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 220 HIS 0.002 0.001 HIS D 284 PHE 0.023 0.002 PHE C 282 TYR 0.012 0.001 TYR C 245 ARG 0.001 0.000 ARG D 194 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2268.36 seconds wall clock time: 43 minutes 6.03 seconds (2586.03 seconds total)