Starting phenix.real_space_refine on Fri Jul 3 07:07:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d65_27217/07_2026/8d65_27217.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d65_27217/07_2026/8d65_27217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d65_27217/07_2026/8d65_27217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d65_27217/07_2026/8d65_27217.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8d65_27217/07_2026/8d65_27217.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d65_27217/07_2026/8d65_27217.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d65_27217/07_2026/8d65_27217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d65_27217/07_2026/8d65_27217.map" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 30 5.16 5 C 8365 2.51 5 N 2080 2.21 5 O 2300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12780 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "B" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "C" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "D" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "E" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.67, per 1000 atoms: 0.21 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: 1.00 Conformation dependent library (CDL) restraints added in 583.6 milliseconds 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 15 sheets defined 33.6% alpha, 35.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 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: 1.65 Time building geometry restraints manager: 1.30 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: 7250 24.04 - 48.08: 340 48.08 - 72.13: 80 72.13 - 96.17: 15 96.17 - 120.21: 10 Dihedral angle restraints: 7695 sinusoidal: 3190 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 7692 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: 0.04 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: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.190 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 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 : 15.703 120.209 4785 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.22 (0.19), residues: 1525 helix: -2.12 (0.18), residues: 530 sheet: -1.23 (0.24), residues: 505 loop : -2.83 (0.24), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 117 TYR 0.009 0.002 TYR B 245 PHE 0.017 0.003 PHE E 304 TRP 0.008 0.002 TRP B 206 HIS 0.004 0.001 HIS C 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00962 / 0.49 (13115) covalent geometry : angle 1.02788 / 0.61 (17815) hydrogen bonds : bond 0.12406 / 8.26 ( 565) hydrogen bonds : angle 6.29238 / 4.33 ( 1770) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.445 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: 0.1104 time to fit residues: 25.1450 Evaluate side-chains 102 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.0870 chunk 91 optimal weight: 0.0040 chunk 149 optimal weight: 2.9990 overall best weight: 0.4570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 ASN A 184 ASN A 185 GLN A 264 GLN B 177 HIS B 184 ASN B 185 GLN B 264 GLN C 184 ASN C 185 GLN D 184 ASN D 185 GLN E 184 ASN E 185 GLN E 264 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.139796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.105462 restraints weight = 14313.988| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.69 r_work: 0.3144 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1560 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= 0.098 Angle : 0.475 5.278 17815 Z= 0.252 Chirality : 0.045 0.135 1960 Planarity : 0.004 0.037 2250 Dihedral : 10.292 69.240 1855 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.16 % Allowed : 8.95 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.21), residues: 1525 helix: -0.12 (0.22), residues: 520 sheet: -0.57 (0.24), residues: 505 loop : -2.40 (0.23), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 255 TYR 0.012 0.001 TYR B 248 PHE 0.036 0.001 PHE E 247 TRP 0.007 0.001 TRP D 220 HIS 0.001 0.000 HIS A 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (13115) covalent geometry : angle 0.47539 / 0.25 (17815) hydrogen bonds : bond 0.02885 / 1.94 ( 565) hydrogen bonds : angle 4.28443 / 2.98 ( 1770) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.481 Fit side-chains REVERT: A 90 LYS cc_start: 0.9317 (pttt) cc_final: 0.8965 (pttm) REVERT: A 149 THR cc_start: 0.9189 (p) cc_final: 0.8968 (t) REVERT: A 245 TYR cc_start: 0.8987 (t80) cc_final: 0.8236 (t80) REVERT: B 226 GLU cc_start: 0.7800 (mp0) cc_final: 0.7393 (mp0) REVERT: C 90 LYS cc_start: 0.9317 (pttt) cc_final: 0.8959 (pttm) REVERT: C 208 PHE cc_start: 0.9176 (m-80) cc_final: 0.8884 (m-80) REVERT: D 149 THR cc_start: 0.9301 (p) cc_final: 0.8945 (t) REVERT: D 245 TYR cc_start: 0.8951 (t80) cc_final: 0.8412 (t80) REVERT: E 86 ASP cc_start: 0.8424 (m-30) cc_final: 0.8187 (m-30) REVERT: E 149 THR cc_start: 0.9209 (p) cc_final: 0.8908 (t) outliers start: 16 outliers final: 7 residues processed: 134 average time/residue: 0.0889 time to fit residues: 19.3282 Evaluate side-chains 107 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain E residue 64 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 87 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 141 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 71 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 ASN B 60 ASN C 264 GLN D 264 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.134007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.103143 restraints weight = 14416.736| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.52 r_work: 0.2927 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1735 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= 0.181 Angle : 0.516 5.239 17815 Z= 0.271 Chirality : 0.047 0.172 1960 Planarity : 0.004 0.033 2250 Dihedral : 9.180 73.229 1855 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.45 % Allowed : 11.20 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.22), residues: 1525 helix: 0.49 (0.23), residues: 530 sheet: -0.26 (0.24), residues: 505 loop : -2.16 (0.24), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 255 TYR 0.009 0.001 TYR C 248 PHE 0.037 0.002 PHE E 247 TRP 0.010 0.001 TRP D 220 HIS 0.003 0.001 HIS B 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.18 (13115) covalent geometry : angle 0.51555 / 0.27 (17815) hydrogen bonds : bond 0.03340 / 2.23 ( 565) hydrogen bonds : angle 4.02775 / 2.80 ( 1770) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.477 Fit side-chains REVERT: A 90 LYS cc_start: 0.9276 (pttt) cc_final: 0.8882 (pttm) REVERT: A 245 TYR cc_start: 0.9079 (t80) cc_final: 0.8285 (t80) REVERT: B 226 GLU cc_start: 0.7753 (mp0) cc_final: 0.7391 (mp0) REVERT: D 115 ASP cc_start: 0.8528 (t70) cc_final: 0.8313 (t0) REVERT: D 236 PHE cc_start: 0.8994 (m-80) cc_final: 0.8731 (m-80) REVERT: D 245 TYR cc_start: 0.8926 (t80) cc_final: 0.8310 (t80) REVERT: E 86 ASP cc_start: 0.8195 (m-30) cc_final: 0.7902 (m-30) outliers start: 20 outliers final: 15 residues processed: 123 average time/residue: 0.0882 time to fit residues: 17.6467 Evaluate side-chains 116 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 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 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 Chi-restraints excluded: chain E residue 189 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 74 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 118 optimal weight: 20.0000 chunk 27 optimal weight: 0.0030 chunk 33 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.132047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.101382 restraints weight = 14508.490| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.54 r_work: 0.3092 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13115 Z= 0.215 Angle : 0.532 5.872 17815 Z= 0.280 Chirality : 0.048 0.156 1960 Planarity : 0.004 0.031 2250 Dihedral : 9.118 78.481 1855 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.82 % Allowed : 12.51 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.22), residues: 1525 helix: 0.75 (0.24), residues: 535 sheet: -0.12 (0.25), residues: 505 loop : -2.04 (0.24), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 105 TYR 0.010 0.001 TYR D 38 PHE 0.032 0.002 PHE E 247 TRP 0.012 0.001 TRP D 220 HIS 0.003 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.22 (13115) covalent geometry : angle 0.53194 / 0.28 (17815) hydrogen bonds : bond 0.03438 / 2.30 ( 565) hydrogen bonds : angle 3.97564 / 2.76 ( 1770) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.473 Fit side-chains REVERT: A 90 LYS cc_start: 0.9330 (pttt) cc_final: 0.8954 (pttm) REVERT: A 105 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8491 (ttt180) REVERT: B 226 GLU cc_start: 0.7730 (mp0) cc_final: 0.7367 (mp0) REVERT: C 226 GLU cc_start: 0.7893 (mp0) cc_final: 0.7637 (mp0) REVERT: D 94 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8648 (mt) REVERT: D 115 ASP cc_start: 0.8660 (t70) cc_final: 0.8348 (t0) REVERT: D 236 PHE cc_start: 0.9072 (m-80) cc_final: 0.8830 (m-80) REVERT: E 86 ASP cc_start: 0.8356 (m-30) cc_final: 0.8088 (m-30) outliers start: 25 outliers final: 16 residues processed: 127 average time/residue: 0.0842 time to fit residues: 17.5147 Evaluate side-chains 119 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 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 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 Chi-restraints excluded: chain E residue 189 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 0.0030 chunk 14 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.167221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.137828 restraints weight = 13546.271| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.70 r_work: 0.3091 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2202 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= 0.106 Angle : 0.449 4.891 17815 Z= 0.235 Chirality : 0.045 0.138 1960 Planarity : 0.003 0.029 2250 Dihedral : 8.410 74.754 1855 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.24 % Allowed : 13.45 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.23), residues: 1525 helix: 1.23 (0.24), residues: 530 sheet: 0.15 (0.25), residues: 505 loop : -1.97 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 91 TYR 0.007 0.001 TYR E 38 PHE 0.029 0.001 PHE E 247 TRP 0.011 0.001 TRP D 220 HIS 0.002 0.000 HIS D 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (13115) covalent geometry : angle 0.44908 / 0.24 (17815) hydrogen bonds : bond 0.02814 / 1.88 ( 565) hydrogen bonds : angle 3.69526 / 2.55 ( 1770) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.551 Fit side-chains REVERT: A 90 LYS cc_start: 0.9286 (pttt) cc_final: 0.8902 (pttm) REVERT: A 245 TYR cc_start: 0.9012 (t80) cc_final: 0.8114 (t80) REVERT: B 226 GLU cc_start: 0.7811 (mp0) cc_final: 0.7436 (mp0) REVERT: C 226 GLU cc_start: 0.7864 (mp0) cc_final: 0.7481 (mp0) REVERT: D 94 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8624 (mt) REVERT: D 236 PHE cc_start: 0.9005 (m-80) cc_final: 0.8754 (m-80) REVERT: D 245 TYR cc_start: 0.8883 (t80) cc_final: 0.8351 (t80) REVERT: E 86 ASP cc_start: 0.8338 (m-30) cc_final: 0.8024 (m-30) outliers start: 17 outliers final: 13 residues processed: 133 average time/residue: 0.0844 time to fit residues: 18.6535 Evaluate side-chains 118 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 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 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 9 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 27 optimal weight: 0.1980 chunk 77 optimal weight: 9.9990 chunk 71 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.137037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.107115 restraints weight = 14229.124| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.51 r_work: 0.3135 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13115 Z= 0.090 Angle : 0.430 4.880 17815 Z= 0.224 Chirality : 0.044 0.134 1960 Planarity : 0.003 0.028 2250 Dihedral : 7.952 71.286 1855 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.31 % Allowed : 14.33 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.23), residues: 1525 helix: 1.51 (0.24), residues: 530 sheet: 0.41 (0.25), residues: 505 loop : -1.86 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 91 TYR 0.008 0.001 TYR B 245 PHE 0.034 0.001 PHE D 247 TRP 0.012 0.001 TRP D 220 HIS 0.001 0.000 HIS D 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.09 (13115) covalent geometry : angle 0.43005 / 0.22 (17815) hydrogen bonds : bond 0.02647 / 1.76 ( 565) hydrogen bonds : angle 3.55708 / 2.45 ( 1770) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.460 Fit side-chains REVERT: A 105 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8525 (ttt180) REVERT: A 245 TYR cc_start: 0.8928 (t80) cc_final: 0.8000 (t80) REVERT: C 226 GLU cc_start: 0.7830 (mp0) cc_final: 0.7460 (mp0) REVERT: D 94 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8596 (mt) REVERT: D 245 TYR cc_start: 0.8858 (t80) cc_final: 0.8295 (t80) REVERT: D 265 MET cc_start: 0.8136 (mtt) cc_final: 0.7825 (mtp) REVERT: E 86 ASP cc_start: 0.8371 (m-30) cc_final: 0.8087 (m-30) REVERT: E 265 MET cc_start: 0.7989 (mtt) cc_final: 0.7692 (mtp) outliers start: 18 outliers final: 11 residues processed: 125 average time/residue: 0.0748 time to fit residues: 15.5687 Evaluate side-chains 112 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ARG 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 250 SER 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 134 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 87 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.129074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.098493 restraints weight = 14569.501| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.45 r_work: 0.2859 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 13115 Z= 0.315 Angle : 0.610 7.422 17815 Z= 0.320 Chirality : 0.052 0.163 1960 Planarity : 0.004 0.034 2250 Dihedral : 9.036 85.466 1855 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.38 % Allowed : 15.05 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.22), residues: 1525 helix: 1.15 (0.24), residues: 530 sheet: -0.10 (0.25), residues: 500 loop : -1.90 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 99 TYR 0.014 0.002 TYR D 38 PHE 0.031 0.003 PHE D 247 TRP 0.018 0.002 TRP D 220 HIS 0.005 0.001 HIS B 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00800 / 0.32 (13115) covalent geometry : angle 0.60991 / 0.32 (17815) hydrogen bonds : bond 0.03971 / 2.67 ( 565) hydrogen bonds : angle 4.01083 / 2.77 ( 1770) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.412 Fit side-chains REVERT: B 156 GLU cc_start: 0.7519 (mp0) cc_final: 0.6488 (tm-30) REVERT: C 226 GLU cc_start: 0.7848 (mp0) cc_final: 0.7589 (mp0) REVERT: E 86 ASP cc_start: 0.8251 (m-30) cc_final: 0.7964 (m-30) REVERT: E 90 LYS cc_start: 0.9241 (pttt) cc_final: 0.8952 (pttm) outliers start: 19 outliers final: 15 residues processed: 115 average time/residue: 0.0822 time to fit residues: 15.4783 Evaluate side-chains 107 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain E residue 189 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 53 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.132665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.102264 restraints weight = 14284.056| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.43 r_work: 0.2916 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13115 Z= 0.153 Angle : 0.490 5.146 17815 Z= 0.257 Chirality : 0.047 0.146 1960 Planarity : 0.004 0.029 2250 Dihedral : 8.449 83.657 1855 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.24 % Allowed : 15.56 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.23), residues: 1525 helix: 1.39 (0.24), residues: 530 sheet: 0.14 (0.25), residues: 505 loop : -1.98 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 194 TYR 0.009 0.001 TYR A 102 PHE 0.036 0.002 PHE D 247 TRP 0.016 0.001 TRP D 220 HIS 0.003 0.001 HIS B 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.15 (13115) covalent geometry : angle 0.49011 / 0.26 (17815) hydrogen bonds : bond 0.03098 / 2.09 ( 565) hydrogen bonds : angle 3.76457 / 2.60 ( 1770) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.496 Fit side-chains REVERT: A 90 LYS cc_start: 0.9253 (pttt) cc_final: 0.8839 (pttm) REVERT: C 226 GLU cc_start: 0.7808 (mp0) cc_final: 0.7546 (mp0) REVERT: E 28 THR cc_start: 0.8952 (p) cc_final: 0.8663 (p) REVERT: E 86 ASP cc_start: 0.8264 (m-30) cc_final: 0.7960 (m-30) outliers start: 17 outliers final: 15 residues processed: 123 average time/residue: 0.0823 time to fit residues: 16.7634 Evaluate side-chains 117 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 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 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 0 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 0.0470 chunk 99 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 131 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 overall best weight: 1.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.135611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.104982 restraints weight = 14258.452| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.58 r_work: 0.3206 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13115 Z= 0.104 Angle : 0.448 4.865 17815 Z= 0.234 Chirality : 0.045 0.136 1960 Planarity : 0.003 0.028 2250 Dihedral : 7.882 81.352 1855 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.38 % Allowed : 15.49 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.23), residues: 1525 helix: 1.64 (0.24), residues: 530 sheet: 0.14 (0.26), residues: 475 loop : -1.52 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 194 TYR 0.008 0.001 TYR A 102 PHE 0.031 0.002 PHE D 247 TRP 0.015 0.001 TRP D 220 HIS 0.001 0.000 HIS D 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.10 (13115) covalent geometry : angle 0.44824 / 0.23 (17815) hydrogen bonds : bond 0.02719 / 1.82 ( 565) hydrogen bonds : angle 3.57657 / 2.46 ( 1770) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.474 Fit side-chains REVERT: A 90 LYS cc_start: 0.9294 (pttt) cc_final: 0.8927 (pttm) REVERT: A 245 TYR cc_start: 0.8977 (t80) cc_final: 0.8056 (t80) REVERT: C 226 GLU cc_start: 0.7850 (mp0) cc_final: 0.7458 (mp0) REVERT: C 265 MET cc_start: 0.7999 (mtt) cc_final: 0.7774 (mtp) REVERT: D 245 TYR cc_start: 0.8908 (t80) cc_final: 0.8378 (t80) REVERT: D 265 MET cc_start: 0.8143 (mtt) cc_final: 0.7831 (mtp) REVERT: E 86 ASP cc_start: 0.8361 (m-30) cc_final: 0.8083 (m-30) REVERT: E 265 MET cc_start: 0.7949 (mtt) cc_final: 0.7658 (mtp) outliers start: 19 outliers final: 16 residues processed: 121 average time/residue: 0.0835 time to fit residues: 16.8160 Evaluate side-chains 115 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 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 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 46 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 72 optimal weight: 0.2980 chunk 49 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 17 optimal weight: 0.0370 overall best weight: 0.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.160437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.126250 restraints weight = 13866.709| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.69 r_work: 0.3135 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13115 Z= 0.094 Angle : 0.440 4.835 17815 Z= 0.229 Chirality : 0.045 0.134 1960 Planarity : 0.003 0.029 2250 Dihedral : 7.523 78.699 1855 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.09 % Allowed : 15.93 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.23), residues: 1525 helix: 1.91 (0.24), residues: 525 sheet: 0.33 (0.26), residues: 485 loop : -1.40 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 117 TYR 0.010 0.001 TYR C 245 PHE 0.026 0.001 PHE D 247 TRP 0.016 0.001 TRP D 220 HIS 0.001 0.000 HIS D 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.09 (13115) covalent geometry : angle 0.44048 / 0.23 (17815) hydrogen bonds : bond 0.02569 / 1.72 ( 565) hydrogen bonds : angle 3.41816 / 2.35 ( 1770) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.495 Fit side-chains REVERT: A 90 LYS cc_start: 0.9234 (pttt) cc_final: 0.8842 (pttm) REVERT: A 245 TYR cc_start: 0.8838 (t80) cc_final: 0.7920 (t80) REVERT: C 226 GLU cc_start: 0.7787 (mp0) cc_final: 0.7425 (mp0) REVERT: C 265 MET cc_start: 0.7845 (mtt) cc_final: 0.7631 (mtp) REVERT: D 245 TYR cc_start: 0.8806 (t80) cc_final: 0.8316 (t80) REVERT: E 86 ASP cc_start: 0.8298 (m-30) cc_final: 0.8005 (m-30) REVERT: E 265 MET cc_start: 0.7755 (mtt) cc_final: 0.7476 (mtp) outliers start: 15 outliers final: 13 residues processed: 122 average time/residue: 0.0819 time to fit residues: 16.6398 Evaluate side-chains 115 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 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 134 SER 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 18 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 147 optimal weight: 0.0010 chunk 135 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.131070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.100858 restraints weight = 14408.857| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.52 r_work: 0.2891 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2614 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= 0.215 Angle : 0.534 6.185 17815 Z= 0.279 Chirality : 0.049 0.152 1960 Planarity : 0.004 0.030 2250 Dihedral : 8.260 85.716 1855 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.31 % Allowed : 16.07 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.22), residues: 1525 helix: 1.62 (0.24), residues: 530 sheet: 0.38 (0.25), residues: 505 loop : -1.93 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 194 TYR 0.010 0.001 TYR D 38 PHE 0.033 0.002 PHE D 247 TRP 0.022 0.001 TRP D 220 HIS 0.003 0.001 HIS D 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.22 (13115) covalent geometry : angle 0.53362 / 0.28 (17815) hydrogen bonds : bond 0.03420 / 2.29 ( 565) hydrogen bonds : angle 3.72913 / 2.58 ( 1770) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2567.76 seconds wall clock time: 44 minutes 45.58 seconds (2685.58 seconds total)