Starting phenix.real_space_refine on Wed Jul 30 21:08:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d65_27217/07_2025/8d65_27217.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d65_27217/07_2025/8d65_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_27217/07_2025/8d65_27217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d65_27217/07_2025/8d65_27217.map" model { file = "/net/cci-nas-00/data/ceres_data/8d65_27217/07_2025/8d65_27217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d65_27217/07_2025/8d65_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 9.05, per 1000 atoms: 0.71 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: 3.38 Conformation dependent library (CDL) restraints added in 1.8 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: 1.55 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: 4.51 Time building geometry restraints manager: 4.04 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 1.020 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: 0.110 Process input model: 33.650 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.060 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.550 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.12406 ( 565) hydrogen bonds : angle 6.29238 ( 1770) covalent geometry : bond 0.00962 (13115) covalent geometry : angle 1.02788 (17815) *********************** 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 : 1.295 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: 0.2663 time to fit residues: 60.2638 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 : 1.232 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.139079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.107905 restraints weight = 14122.425| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.46 r_work: 0.2956 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 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= 0.114 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 Details of bonding type rmsd hydrogen bonds : bond 0.03104 ( 565) hydrogen bonds : angle 4.33987 ( 1770) covalent geometry : bond 0.00268 (13115) covalent geometry : angle 0.49003 (17815) *********************** 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 : 1.471 Fit side-chains REVERT: A 90 LYS cc_start: 0.9273 (pttt) cc_final: 0.8898 (pttm) REVERT: A 149 THR cc_start: 0.9185 (p) cc_final: 0.8970 (t) REVERT: A 245 TYR cc_start: 0.9068 (t80) cc_final: 0.8312 (t80) REVERT: B 226 GLU cc_start: 0.7703 (mp0) cc_final: 0.7286 (mp0) REVERT: C 90 LYS cc_start: 0.9283 (pttt) cc_final: 0.8987 (pttm) REVERT: D 245 TYR cc_start: 0.8946 (t80) cc_final: 0.8364 (t80) REVERT: E 86 ASP cc_start: 0.8337 (m-30) cc_final: 0.8063 (m-30) REVERT: E 282 PHE cc_start: 0.8188 (t80) cc_final: 0.7950 (t80) outliers start: 16 outliers final: 7 residues processed: 127 average time/residue: 0.1947 time to fit residues: 39.9674 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 : 1.481 ------------------------------------------------------------------------------- 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 39 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 135 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 116 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 = 0.3371 r_free = 0.3371 target = 0.130902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.100323 restraints weight = 14544.139| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.58 r_work: 0.3090 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 13115 Z= 0.257 Angle : 0.583 6.335 17815 Z= 0.308 Chirality : 0.049 0.198 1960 Planarity : 0.004 0.034 2250 Dihedral : 10.937 79.400 1920 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.75 % Allowed : 11.35 % Favored : 86.91 % 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: -1.21 (0.21), residues: 1525 helix: 0.34 (0.23), residues: 530 sheet: -0.77 (0.25), residues: 475 loop : -1.91 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 220 HIS 0.003 0.001 HIS D 284 PHE 0.041 0.002 PHE E 247 TYR 0.011 0.002 TYR D 38 ARG 0.003 0.000 ARG C 255 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 565) hydrogen bonds : angle 4.20316 ( 1770) covalent geometry : bond 0.00640 (13115) covalent geometry : angle 0.58349 (17815) *********************** 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 127 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 1.214 Fit side-chains REVERT: A 90 LYS cc_start: 0.9267 (pttt) cc_final: 0.8899 (pttm) REVERT: B 226 GLU cc_start: 0.7793 (mp0) cc_final: 0.7414 (mp0) REVERT: C 226 GLU cc_start: 0.7912 (mp0) cc_final: 0.7648 (mp0) REVERT: D 94 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8653 (mt) REVERT: D 150 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7217 (mt-10) REVERT: D 226 GLU cc_start: 0.7829 (mp0) cc_final: 0.7415 (mp0) REVERT: E 86 ASP cc_start: 0.8408 (m-30) cc_final: 0.8137 (m-30) REVERT: E 90 LYS cc_start: 0.9298 (pttt) cc_final: 0.9030 (pttm) REVERT: E 282 PHE cc_start: 0.8310 (t80) cc_final: 0.8039 (t80) outliers start: 24 outliers final: 18 residues processed: 125 average time/residue: 0.2029 time to fit residues: 40.4046 Evaluate side-chains 118 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 1.424 ------------------------------------------------------------------------------- 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 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 93 MET 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 94 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 150 GLU 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 81 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.134388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.104627 restraints weight = 14233.847| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.49 r_work: 0.3093 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13115 Z= 0.126 Angle : 0.467 5.169 17815 Z= 0.246 Chirality : 0.046 0.141 1960 Planarity : 0.003 0.031 2250 Dihedral : 10.072 74.921 1920 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.67 % Allowed : 12.73 % Favored : 85.60 % 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: -0.53 (0.22), residues: 1525 helix: 0.94 (0.24), residues: 530 sheet: -0.04 (0.25), residues: 505 loop : -2.10 (0.24), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 220 HIS 0.002 0.001 HIS B 284 PHE 0.037 0.001 PHE E 247 TYR 0.007 0.001 TYR D 38 ARG 0.002 0.000 ARG C 255 Details of bonding type rmsd hydrogen bonds : bond 0.02982 ( 565) hydrogen bonds : angle 3.84100 ( 1770) covalent geometry : bond 0.00307 (13115) covalent geometry : angle 0.46749 (17815) *********************** 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 139 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 2.720 Fit side-chains REVERT: A 90 LYS cc_start: 0.9259 (pttt) cc_final: 0.8879 (pttm) REVERT: A 245 TYR cc_start: 0.9043 (t80) cc_final: 0.8158 (t80) REVERT: B 226 GLU cc_start: 0.7769 (mp0) cc_final: 0.7404 (mp0) REVERT: B 256 LEU cc_start: 0.8838 (mt) cc_final: 0.8616 (mt) REVERT: C 226 GLU cc_start: 0.7862 (mp0) cc_final: 0.7621 (mp0) REVERT: D 94 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8610 (mt) REVERT: D 226 GLU cc_start: 0.7825 (mp0) cc_final: 0.7394 (mp0) REVERT: D 236 PHE cc_start: 0.9044 (m-80) cc_final: 0.8807 (m-80) REVERT: D 245 TYR cc_start: 0.8901 (t80) cc_final: 0.8345 (t80) REVERT: D 247 PHE cc_start: 0.8666 (t80) cc_final: 0.8130 (t80) REVERT: E 86 ASP cc_start: 0.8319 (m-30) cc_final: 0.8022 (m-30) REVERT: E 282 PHE cc_start: 0.8259 (t80) cc_final: 0.8043 (t80) outliers start: 23 outliers final: 16 residues processed: 136 average time/residue: 0.2182 time to fit residues: 49.1315 Evaluate side-chains 123 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 1.804 ------------------------------------------------------------------------------- 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 129 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 chunk 100 optimal weight: 0.4980 chunk 135 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.156127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.120509 restraints weight = 13936.470| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.79 r_work: 0.3094 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13115 Z= 0.093 Angle : 0.434 4.838 17815 Z= 0.227 Chirality : 0.044 0.133 1960 Planarity : 0.003 0.030 2250 Dihedral : 9.373 71.014 1920 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.09 % Allowed : 13.31 % Favored : 85.60 % 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: -0.02 (0.23), residues: 1525 helix: 1.34 (0.24), residues: 530 sheet: 0.35 (0.25), residues: 505 loop : -1.92 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 220 HIS 0.001 0.000 HIS B 284 PHE 0.029 0.001 PHE D 247 TYR 0.015 0.001 TYR B 245 ARG 0.001 0.000 ARG D 91 Details of bonding type rmsd hydrogen bonds : bond 0.02687 ( 565) hydrogen bonds : angle 3.61081 ( 1770) covalent geometry : bond 0.00217 (13115) covalent geometry : angle 0.43433 (17815) *********************** 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 134 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 1.737 Fit side-chains REVERT: A 245 TYR cc_start: 0.8949 (t80) cc_final: 0.8041 (t80) REVERT: B 226 GLU cc_start: 0.7740 (mp0) cc_final: 0.7351 (mp0) REVERT: C 226 GLU cc_start: 0.7788 (mp0) cc_final: 0.7414 (mp0) REVERT: D 245 TYR cc_start: 0.8810 (t80) cc_final: 0.8266 (t80) REVERT: D 247 PHE cc_start: 0.8608 (t80) cc_final: 0.8279 (t80) REVERT: D 265 MET cc_start: 0.8061 (mtt) cc_final: 0.7761 (mtp) REVERT: E 86 ASP cc_start: 0.8369 (m-30) cc_final: 0.8078 (m-30) REVERT: E 265 MET cc_start: 0.7878 (mtt) cc_final: 0.7594 (mtp) REVERT: E 282 PHE cc_start: 0.8202 (t80) cc_final: 0.7979 (t80) outliers start: 15 outliers final: 10 residues processed: 130 average time/residue: 0.2487 time to fit residues: 53.8540 Evaluate side-chains 111 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 250 SER Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 94 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 77 optimal weight: 10.0000 chunk 136 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 121 optimal weight: 0.0070 chunk 146 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 27 optimal weight: 0.0050 chunk 52 optimal weight: 4.9990 overall best weight: 2.0016 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.165257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.134712 restraints weight = 13658.738| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.81 r_work: 0.3093 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13115 Z= 0.156 Angle : 0.482 4.925 17815 Z= 0.251 Chirality : 0.047 0.144 1960 Planarity : 0.003 0.029 2250 Dihedral : 9.518 73.707 1920 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.45 % Allowed : 14.04 % Favored : 84.51 % 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: -0.01 (0.23), residues: 1525 helix: 1.43 (0.24), residues: 530 sheet: 0.04 (0.26), residues: 475 loop : -1.53 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 220 HIS 0.002 0.001 HIS B 284 PHE 0.024 0.002 PHE D 247 TYR 0.015 0.001 TYR B 245 ARG 0.002 0.000 ARG C 255 Details of bonding type rmsd hydrogen bonds : bond 0.03073 ( 565) hydrogen bonds : angle 3.68411 ( 1770) covalent geometry : bond 0.00390 (13115) covalent geometry : angle 0.48155 (17815) *********************** 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 117 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 1.887 Fit side-chains REVERT: B 226 GLU cc_start: 0.7865 (mp0) cc_final: 0.7462 (mp0) REVERT: C 226 GLU cc_start: 0.7880 (mp0) cc_final: 0.7482 (mp0) REVERT: D 94 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8696 (mt) REVERT: E 86 ASP cc_start: 0.8463 (m-30) cc_final: 0.8188 (m-30) REVERT: E 282 PHE cc_start: 0.8260 (t80) cc_final: 0.7980 (t80) outliers start: 20 outliers final: 15 residues processed: 114 average time/residue: 0.2767 time to fit residues: 53.4745 Evaluate side-chains 110 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 3.740 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 46 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 3 optimal weight: 0.0970 chunk 105 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.3457 r_free = 0.3457 target = 0.138073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.110311 restraints weight = 14091.980| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.42 r_work: 0.3208 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13115 Z= 0.090 Angle : 0.428 4.857 17815 Z= 0.223 Chirality : 0.044 0.130 1960 Planarity : 0.003 0.028 2250 Dihedral : 9.002 68.082 1920 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.38 % Allowed : 14.33 % Favored : 84.29 % 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: 0.31 (0.23), residues: 1525 helix: 1.68 (0.24), residues: 530 sheet: 0.33 (0.26), residues: 475 loop : -1.47 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 220 HIS 0.001 0.000 HIS D 177 PHE 0.026 0.001 PHE D 247 TYR 0.012 0.001 TYR B 245 ARG 0.001 0.000 ARG D 194 Details of bonding type rmsd hydrogen bonds : bond 0.02580 ( 565) hydrogen bonds : angle 3.48028 ( 1770) covalent geometry : bond 0.00210 (13115) covalent geometry : angle 0.42841 (17815) *********************** 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 125 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 1.428 Fit side-chains REVERT: A 245 TYR cc_start: 0.8909 (t80) cc_final: 0.8025 (t80) REVERT: C 156 GLU cc_start: 0.7573 (mp0) cc_final: 0.6793 (tm-30) REVERT: C 226 GLU cc_start: 0.7812 (mp0) cc_final: 0.7447 (mp0) REVERT: D 94 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8610 (mt) REVERT: D 245 TYR cc_start: 0.8861 (t80) cc_final: 0.8379 (t80) REVERT: D 265 MET cc_start: 0.8123 (mtt) cc_final: 0.7806 (mtp) REVERT: E 86 ASP cc_start: 0.8405 (m-30) cc_final: 0.8127 (m-30) REVERT: E 265 MET cc_start: 0.7968 (mtt) cc_final: 0.7698 (mtp) REVERT: E 282 PHE cc_start: 0.8256 (t80) cc_final: 0.8002 (t80) outliers start: 19 outliers final: 11 residues processed: 121 average time/residue: 0.1813 time to fit residues: 36.3389 Evaluate side-chains 109 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 55 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 101 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.3385 r_free = 0.3385 target = 0.132060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.101690 restraints weight = 14446.943| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.58 r_work: 0.3027 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2484 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= 0.214 Angle : 0.526 5.691 17815 Z= 0.276 Chirality : 0.049 0.151 1960 Planarity : 0.004 0.029 2250 Dihedral : 9.604 75.787 1920 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.53 % Allowed : 14.69 % 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: 0.05 (0.23), residues: 1525 helix: 1.54 (0.24), residues: 530 sheet: 0.07 (0.25), residues: 475 loop : -1.56 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 220 HIS 0.003 0.001 HIS E 284 PHE 0.032 0.002 PHE D 247 TYR 0.013 0.001 TYR B 245 ARG 0.002 0.000 ARG E 255 Details of bonding type rmsd hydrogen bonds : bond 0.03456 ( 565) hydrogen bonds : angle 3.76005 ( 1770) covalent geometry : bond 0.00539 (13115) covalent geometry : angle 0.52639 (17815) *********************** 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 116 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 2.200 Fit side-chains REVERT: A 90 LYS cc_start: 0.9293 (pttt) cc_final: 0.8912 (pttm) REVERT: C 226 GLU cc_start: 0.7867 (mp0) cc_final: 0.7632 (mp0) REVERT: D 94 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8687 (mt) REVERT: E 86 ASP cc_start: 0.8393 (m-30) cc_final: 0.8110 (m-30) REVERT: E 282 PHE cc_start: 0.8453 (t80) cc_final: 0.8141 (t80) outliers start: 21 outliers final: 15 residues processed: 113 average time/residue: 0.2326 time to fit residues: 43.4832 Evaluate side-chains 108 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 1.631 ------------------------------------------------------------------------------- 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 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 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 141 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 146 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 10 optimal weight: 0.0050 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.137849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.108621 restraints weight = 14127.050| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.54 r_work: 0.3235 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13115 Z= 0.090 Angle : 0.433 4.807 17815 Z= 0.226 Chirality : 0.044 0.131 1960 Planarity : 0.003 0.028 2250 Dihedral : 9.015 68.909 1920 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.31 % Allowed : 14.91 % 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: 0.39 (0.23), residues: 1525 helix: 1.77 (0.24), residues: 530 sheet: 0.38 (0.26), residues: 475 loop : -1.45 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 220 HIS 0.001 0.000 HIS D 177 PHE 0.024 0.001 PHE D 247 TYR 0.010 0.001 TYR B 245 ARG 0.001 0.000 ARG D 194 Details of bonding type rmsd hydrogen bonds : bond 0.02627 ( 565) hydrogen bonds : angle 3.50857 ( 1770) covalent geometry : bond 0.00210 (13115) covalent geometry : angle 0.43295 (17815) *********************** 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 122 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 1.303 Fit side-chains REVERT: A 245 TYR cc_start: 0.8938 (t80) cc_final: 0.7957 (t80) REVERT: C 156 GLU cc_start: 0.7538 (mp0) cc_final: 0.6895 (tm-30) REVERT: C 226 GLU cc_start: 0.7768 (mp0) cc_final: 0.7423 (mp0) REVERT: D 94 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8655 (mt) REVERT: D 245 TYR cc_start: 0.8856 (t80) cc_final: 0.8367 (t80) REVERT: D 247 PHE cc_start: 0.8536 (t80) cc_final: 0.8193 (t80) REVERT: E 86 ASP cc_start: 0.8423 (m-30) cc_final: 0.8126 (m-30) REVERT: E 265 MET cc_start: 0.7905 (mtt) cc_final: 0.7627 (mtp) REVERT: E 282 PHE cc_start: 0.8188 (t80) cc_final: 0.7914 (t80) outliers start: 18 outliers final: 15 residues processed: 119 average time/residue: 0.1779 time to fit residues: 35.2644 Evaluate side-chains 112 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 93 MET 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 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 26 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 135 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 59 optimal weight: 0.0770 chunk 58 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 overall best weight: 0.7744 ------------------------------------------------------------------------------- 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 = 0.3454 r_free = 0.3454 target = 0.138088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.109619 restraints weight = 14190.128| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.45 r_work: 0.2948 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13115 Z= 0.095 Angle : 0.434 4.816 17815 Z= 0.226 Chirality : 0.045 0.134 1960 Planarity : 0.003 0.028 2250 Dihedral : 8.857 69.212 1920 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.24 % Allowed : 15.35 % Favored : 83.42 % 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: 0.62 (0.23), residues: 1525 helix: 2.00 (0.24), residues: 525 sheet: 0.49 (0.26), residues: 485 loop : -1.36 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 220 HIS 0.001 0.000 HIS D 177 PHE 0.024 0.001 PHE A 247 TYR 0.008 0.001 TYR A 245 ARG 0.001 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.02605 ( 565) hydrogen bonds : angle 3.40140 ( 1770) covalent geometry : bond 0.00225 (13115) covalent geometry : angle 0.43394 (17815) ********************** 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 119 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 1.330 Fit side-chains REVERT: B 226 GLU cc_start: 0.7970 (mp0) cc_final: 0.7667 (mp0) REVERT: C 156 GLU cc_start: 0.7474 (mp0) cc_final: 0.6864 (tm-30) REVERT: D 94 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8612 (mt) REVERT: D 247 PHE cc_start: 0.8551 (t80) cc_final: 0.8298 (t80) REVERT: E 86 ASP cc_start: 0.8273 (m-30) cc_final: 0.7957 (m-30) REVERT: E 265 MET cc_start: 0.7796 (mtt) cc_final: 0.7527 (mtp) REVERT: E 282 PHE cc_start: 0.8207 (t80) cc_final: 0.7934 (t80) outliers start: 17 outliers final: 13 residues processed: 117 average time/residue: 0.1746 time to fit residues: 34.3370 Evaluate side-chains 110 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 93 MET 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 E residue 134 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 88 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 87 optimal weight: 0.4980 chunk 134 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3459 r_free = 0.3459 target = 0.138481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.109323 restraints weight = 14072.723| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.55 r_work: 0.2990 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13115 Z= 0.099 Angle : 0.437 4.810 17815 Z= 0.229 Chirality : 0.045 0.144 1960 Planarity : 0.003 0.028 2250 Dihedral : 8.786 68.372 1920 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.24 % Allowed : 15.49 % 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 (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: 0.72 (0.23), residues: 1525 helix: 2.08 (0.24), residues: 525 sheet: 0.56 (0.26), residues: 485 loop : -1.30 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 220 HIS 0.001 0.000 HIS E 284 PHE 0.024 0.001 PHE D 247 TYR 0.010 0.001 TYR B 245 ARG 0.001 0.000 ARG D 194 Details of bonding type rmsd hydrogen bonds : bond 0.02602 ( 565) hydrogen bonds : angle 3.37820 ( 1770) covalent geometry : bond 0.00236 (13115) covalent geometry : angle 0.43690 (17815) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6112.60 seconds wall clock time: 111 minutes 33.78 seconds (6693.78 seconds total)