Starting phenix.real_space_refine on Wed Mar 4 10:13:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d63_27215/03_2026/8d63_27215.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d63_27215/03_2026/8d63_27215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d63_27215/03_2026/8d63_27215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d63_27215/03_2026/8d63_27215.map" model { file = "/net/cci-nas-00/data/ceres_data/8d63_27215/03_2026/8d63_27215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d63_27215/03_2026/8d63_27215.cif" } resolution = 3.14 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= 0.012 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 8375 2.51 5 N 2085 2.21 5 O 2290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12785 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: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'LBN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'LBN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'LBN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'LBN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'LBN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.00, per 1000 atoms: 0.23 Number of scatterers: 12785 At special positions: 0 Unit cell: (92.4, 91.3, 122.1, 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 2290 8.00 N 2085 7.00 C 8375 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: 1.03 Conformation dependent library (CDL) restraints added in 580.5 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 34.9% alpha, 35.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 61 through 69 removed outlier: 3.943A pdb=" N ARG A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN A 69 " --> pdb=" O ARG A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.697A pdb=" N SER A 179 " --> pdb=" O ASP A 176 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER A 180 " --> pdb=" O HIS A 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 176 through 180' Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 208 through 220 removed outlier: 3.730A pdb=" N LEU A 212 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 252 removed outlier: 3.723A pdb=" N ILE A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 286 Processing helix chain 'A' and resid 296 through 300 removed outlier: 3.563A 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 61 through 69 removed outlier: 3.943A pdb=" N ARG B 65 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN B 69 " --> pdb=" O ARG B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 removed outlier: 3.697A pdb=" N SER B 179 " --> pdb=" O ASP B 176 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER B 180 " --> pdb=" O HIS B 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 176 through 180' Processing helix chain 'B' and resid 201 through 208 Processing helix chain 'B' and resid 208 through 220 removed outlier: 3.730A pdb=" N LEU B 212 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 252 removed outlier: 3.723A pdb=" N ILE B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 286 Processing helix chain 'B' and resid 296 through 300 removed outlier: 3.563A 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 61 through 69 removed outlier: 3.943A pdb=" N ARG C 65 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN C 69 " --> pdb=" O ARG C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 180 removed outlier: 3.697A pdb=" N SER C 179 " --> pdb=" O ASP C 176 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER C 180 " --> pdb=" O HIS C 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 176 through 180' Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'C' and resid 208 through 220 removed outlier: 3.730A pdb=" N LEU C 212 " --> pdb=" O PHE C 208 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRP C 220 " --> pdb=" O ILE C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 252 removed outlier: 3.723A pdb=" N ILE C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 286 Processing helix chain 'C' and resid 296 through 300 removed outlier: 3.563A 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 61 through 69 removed outlier: 3.942A pdb=" N ARG D 65 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN D 69 " --> pdb=" O ARG D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 180 removed outlier: 3.697A pdb=" N SER D 179 " --> pdb=" O ASP D 176 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER D 180 " --> pdb=" O HIS D 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 176 through 180' Processing helix chain 'D' and resid 201 through 208 Processing helix chain 'D' and resid 208 through 220 removed outlier: 3.730A pdb=" N LEU D 212 " --> pdb=" O PHE D 208 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP D 220 " --> pdb=" O ILE D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 252 removed outlier: 3.723A pdb=" N ILE D 252 " --> pdb=" O TYR D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 286 Processing helix chain 'D' and resid 296 through 300 removed outlier: 3.563A 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 61 through 69 removed outlier: 3.943A pdb=" N ARG E 65 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN E 69 " --> pdb=" O ARG E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 180 removed outlier: 3.697A pdb=" N SER E 179 " --> pdb=" O ASP E 176 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER E 180 " --> pdb=" O HIS E 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 176 through 180' Processing helix chain 'E' and resid 201 through 208 Processing helix chain 'E' and resid 208 through 220 removed outlier: 3.730A pdb=" N LEU E 212 " --> pdb=" O PHE E 208 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRP E 220 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 252 removed outlier: 3.723A pdb=" N ILE E 252 " --> pdb=" O TYR E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 286 Processing helix chain 'E' and resid 296 through 300 removed outlier: 3.563A 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 58 removed outlier: 6.381A pdb=" N THR A 32 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY A 25 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N THR A 44 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP A 13 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 9.648A pdb=" N VAL A 12 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N ASP A 144 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL A 14 " --> pdb=" O ASP A 144 " (cutoff:3.500A) removed outlier: 8.894A pdb=" N GLN A 146 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL A 16 " --> pdb=" O GLN A 146 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N TYR A 148 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE A 18 " --> pdb=" O TYR A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.731A 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: 6.731A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 56 through 58 removed outlier: 6.381A pdb=" N THR B 32 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY B 25 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N THR B 44 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ASP B 13 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 9.648A pdb=" N VAL B 12 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N ASP B 144 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL B 14 " --> pdb=" O ASP B 144 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N GLN B 146 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 16 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N TYR B 148 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE B 18 " --> pdb=" O TYR B 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.731A 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: 6.731A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 58 removed outlier: 6.381A pdb=" N THR C 32 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY C 25 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N THR C 44 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ASP C 13 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 9.648A pdb=" N VAL C 12 " --> pdb=" O PHE C 142 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N ASP C 144 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL C 14 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N GLN C 146 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL C 16 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N TYR C 148 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE C 18 " --> pdb=" O TYR C 148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.731A 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: 6.731A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 56 through 58 removed outlier: 6.381A pdb=" N THR D 32 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY D 25 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LYS D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE D 23 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASP D 36 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N THR D 44 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP D 13 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 9.648A pdb=" N VAL D 12 " --> pdb=" O PHE D 142 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N ASP D 144 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL D 14 " --> pdb=" O ASP D 144 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N GLN D 146 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL D 16 " --> pdb=" O GLN D 146 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N TYR D 148 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE D 18 " --> pdb=" O TYR D 148 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.731A 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: 6.731A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 56 through 58 removed outlier: 6.381A pdb=" N THR E 32 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY E 25 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N THR E 44 " --> pdb=" O ASP E 13 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP E 13 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 9.648A pdb=" N VAL E 12 " --> pdb=" O PHE E 142 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N ASP E 144 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL E 14 " --> pdb=" O ASP E 144 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N GLN E 146 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL E 16 " --> pdb=" O GLN E 146 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N TYR E 148 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE E 18 " --> pdb=" O TYR E 148 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.731A 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: 6.731A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1845 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.18 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2015 1.31 - 1.43: 3755 1.43 - 1.56: 7223 1.56 - 1.68: 77 1.68 - 1.81: 50 Bond restraints: 13120 Sorted by residual: bond pdb=" C34 LBN C 401 " pdb=" O7 LBN C 401 " ideal model delta sigma weight residual 1.331 1.427 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C34 LBN B 401 " pdb=" O7 LBN B 401 " ideal model delta sigma weight residual 1.331 1.426 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C34 LBN E 401 " pdb=" O7 LBN E 401 " ideal model delta sigma weight residual 1.331 1.426 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C34 LBN D 401 " pdb=" O7 LBN D 401 " ideal model delta sigma weight residual 1.331 1.426 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C34 LBN A 401 " pdb=" O7 LBN A 401 " ideal model delta sigma weight residual 1.331 1.426 -0.095 2.00e-02 2.50e+03 2.25e+01 ... (remaining 13115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 17537 3.20 - 6.40: 228 6.40 - 9.60: 55 9.60 - 12.80: 5 12.80 - 15.99: 5 Bond angle restraints: 17830 Sorted by residual: angle pdb=" N ASN C 60 " pdb=" CA ASN C 60 " pdb=" C ASN C 60 " ideal model delta sigma weight residual 111.07 119.92 -8.85 1.07e+00 8.73e-01 6.84e+01 angle pdb=" N ASN E 60 " pdb=" CA ASN E 60 " pdb=" C ASN E 60 " ideal model delta sigma weight residual 111.07 119.92 -8.85 1.07e+00 8.73e-01 6.84e+01 angle pdb=" N ASN A 60 " pdb=" CA ASN A 60 " pdb=" C ASN A 60 " ideal model delta sigma weight residual 111.07 119.91 -8.84 1.07e+00 8.73e-01 6.83e+01 angle pdb=" N ASN B 60 " pdb=" CA ASN B 60 " pdb=" C ASN B 60 " ideal model delta sigma weight residual 111.07 119.90 -8.83 1.07e+00 8.73e-01 6.80e+01 angle pdb=" N ASN D 60 " pdb=" CA ASN D 60 " pdb=" C ASN D 60 " ideal model delta sigma weight residual 111.07 119.87 -8.80 1.07e+00 8.73e-01 6.77e+01 ... (remaining 17825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.58: 7170 21.58 - 43.15: 435 43.15 - 64.73: 100 64.73 - 86.31: 25 86.31 - 107.88: 20 Dihedral angle restraints: 7750 sinusoidal: 3245 harmonic: 4505 Sorted by residual: dihedral pdb=" CA LEU B 118 " pdb=" C LEU B 118 " pdb=" N PHE B 119 " pdb=" CA PHE B 119 " ideal model delta harmonic sigma weight residual -180.00 -156.48 -23.52 0 5.00e+00 4.00e-02 2.21e+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 -156.48 -23.52 0 5.00e+00 4.00e-02 2.21e+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 -156.50 -23.50 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 7747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1518 0.064 - 0.129: 353 0.129 - 0.193: 53 0.193 - 0.257: 21 0.257 - 0.322: 10 Chirality restraints: 1955 Sorted by residual: chirality pdb=" CA GLU C 59 " pdb=" N GLU C 59 " pdb=" C GLU C 59 " pdb=" CB GLU C 59 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA GLU D 59 " pdb=" N GLU D 59 " pdb=" C GLU D 59 " pdb=" CB GLU D 59 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA GLU A 59 " pdb=" N GLU A 59 " pdb=" C GLU A 59 " pdb=" CB GLU A 59 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 1952 not shown) Planarity restraints: 2250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 50 " 0.033 5.00e-02 4.00e+02 5.08e-02 4.12e+00 pdb=" N PRO D 51 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 51 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 51 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 50 " 0.033 5.00e-02 4.00e+02 5.07e-02 4.11e+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 delta sigma weight rms_deltas residual plane pdb=" C THR B 50 " 0.033 5.00e-02 4.00e+02 5.07e-02 4.11e+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 ... (remaining 2247 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3431 2.81 - 3.33: 10726 3.33 - 3.86: 19914 3.86 - 4.38: 23566 4.38 - 4.90: 42808 Nonbonded interactions: 100445 Sorted by model distance: nonbonded pdb=" O TYR B 248 " pdb=" CD1 ILE B 252 " model vdw 2.290 3.460 nonbonded pdb=" O TYR D 248 " pdb=" CD1 ILE D 252 " model vdw 2.290 3.460 nonbonded pdb=" O TYR E 248 " pdb=" CD1 ILE E 252 " model vdw 2.291 3.460 nonbonded pdb=" O TYR C 248 " pdb=" CD1 ILE C 252 " model vdw 2.291 3.460 nonbonded pdb=" O TYR A 248 " pdb=" CD1 ILE A 252 " model vdw 2.291 3.460 ... (remaining 100440 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.540 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.096 13120 Z= 0.423 Angle : 0.987 15.995 17830 Z= 0.540 Chirality : 0.062 0.322 1955 Planarity : 0.005 0.051 2250 Dihedral : 16.369 107.881 4840 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.98 % Favored : 94.69 % Rotamer: Outliers : 0.36 % Allowed : 1.45 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.21), residues: 1525 helix: -0.01 (0.21), residues: 530 sheet: 0.04 (0.25), residues: 490 loop : -1.99 (0.23), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 123 TYR 0.011 0.002 TYR A 204 PHE 0.024 0.003 PHE C 247 TRP 0.010 0.002 TRP C 161 HIS 0.007 0.002 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00889 (13120) covalent geometry : angle 0.98660 (17830) hydrogen bonds : bond 0.15565 ( 580) hydrogen bonds : angle 6.33847 ( 1845) *********************** 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 165 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 160 time to evaluate : 0.458 Fit side-chains REVERT: A 163 ARG cc_start: 0.8147 (mmt-90) cc_final: 0.7737 (mmt-90) REVERT: A 245 TYR cc_start: 0.8383 (t80) cc_final: 0.8072 (t80) REVERT: C 61 THR cc_start: 0.8940 (m) cc_final: 0.8676 (p) REVERT: C 206 TRP cc_start: 0.7842 (m100) cc_final: 0.7614 (m100) REVERT: D 150 GLU cc_start: 0.7606 (pt0) cc_final: 0.7236 (pt0) REVERT: E 61 THR cc_start: 0.9014 (m) cc_final: 0.8737 (p) REVERT: E 150 GLU cc_start: 0.7678 (pt0) cc_final: 0.7462 (pt0) REVERT: E 174 ARG cc_start: 0.8206 (ttm-80) cc_final: 0.7964 (ttm170) REVERT: E 177 HIS cc_start: 0.6673 (p90) cc_final: 0.6048 (p90) outliers start: 5 outliers final: 0 residues processed: 161 average time/residue: 0.1353 time to fit residues: 30.3417 Evaluate side-chains 114 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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: 2.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 62 GLN A 151 ASN A 251 ASN B 60 ASN B 62 GLN B 251 ASN C 60 ASN C 62 GLN D 60 ASN D 62 GLN E 60 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.149854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.100859 restraints weight = 13197.332| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.15 r_work: 0.2848 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13120 Z= 0.109 Angle : 0.489 5.579 17830 Z= 0.254 Chirality : 0.045 0.135 1955 Planarity : 0.004 0.035 2250 Dihedral : 14.170 113.322 1910 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.44 % Allowed : 4.29 % Favored : 95.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.22), residues: 1525 helix: 1.23 (0.23), residues: 535 sheet: 0.20 (0.25), residues: 500 loop : -1.71 (0.24), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 255 TYR 0.012 0.001 TYR B 245 PHE 0.023 0.002 PHE A 247 TRP 0.008 0.001 TRP D 206 HIS 0.002 0.001 HIS E 177 Details of bonding type rmsd covalent geometry : bond 0.00259 (13120) covalent geometry : angle 0.48940 (17830) hydrogen bonds : bond 0.03252 ( 580) hydrogen bonds : angle 4.18208 ( 1845) *********************** 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 137 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 131 time to evaluate : 0.489 Fit side-chains REVERT: A 150 GLU cc_start: 0.7796 (pt0) cc_final: 0.7542 (pt0) REVERT: A 163 ARG cc_start: 0.8191 (mmt-90) cc_final: 0.7757 (mmt-90) REVERT: B 60 ASN cc_start: 0.8948 (OUTLIER) cc_final: 0.8646 (m-40) REVERT: B 239 MET cc_start: 0.7439 (ttp) cc_final: 0.6916 (tpp) REVERT: C 163 ARG cc_start: 0.7950 (mmt-90) cc_final: 0.7484 (mmt-90) REVERT: D 150 GLU cc_start: 0.7681 (pt0) cc_final: 0.7421 (pt0) REVERT: E 174 ARG cc_start: 0.8567 (ttm-80) cc_final: 0.8272 (ttm170) outliers start: 6 outliers final: 3 residues processed: 137 average time/residue: 0.1486 time to fit residues: 28.0653 Evaluate side-chains 119 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain E residue 60 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 88 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 58 optimal weight: 30.0000 chunk 17 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN C 60 ASN C 251 ASN D 251 ASN E 60 ASN E 251 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.141422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.092632 restraints weight = 13562.424| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.15 r_work: 0.2725 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.065 13120 Z= 0.366 Angle : 0.681 7.240 17830 Z= 0.353 Chirality : 0.053 0.189 1955 Planarity : 0.005 0.041 2250 Dihedral : 13.914 108.378 1910 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.44 % Allowed : 7.42 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.19 (0.21), residues: 1525 helix: 1.29 (0.22), residues: 540 sheet: -0.06 (0.23), residues: 500 loop : -1.77 (0.24), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 99 TYR 0.015 0.002 TYR D 204 PHE 0.016 0.003 PHE C 247 TRP 0.012 0.002 TRP D 206 HIS 0.007 0.002 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00934 (13120) covalent geometry : angle 0.68102 (17830) hydrogen bonds : bond 0.04560 ( 580) hydrogen bonds : angle 4.27516 ( 1845) *********************** 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: 6 poor density : 119 time to evaluate : 0.496 Fit side-chains REVERT: A 245 TYR cc_start: 0.8609 (t80) cc_final: 0.8256 (t80) REVERT: D 150 GLU cc_start: 0.7847 (pt0) cc_final: 0.7548 (pt0) REVERT: E 174 ARG cc_start: 0.8572 (ttm-80) cc_final: 0.8222 (ttm170) REVERT: E 245 TYR cc_start: 0.8529 (t80) cc_final: 0.8205 (t80) outliers start: 6 outliers final: 6 residues processed: 123 average time/residue: 0.1575 time to fit residues: 26.3998 Evaluate side-chains 108 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 279 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 27 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 147 optimal weight: 0.2980 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.145907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.097158 restraints weight = 13326.850| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.16 r_work: 0.2789 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13120 Z= 0.148 Angle : 0.493 5.336 17830 Z= 0.255 Chirality : 0.046 0.144 1955 Planarity : 0.003 0.033 2250 Dihedral : 12.431 107.163 1910 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.58 % Allowed : 8.58 % Favored : 90.84 % 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: 0.24 (0.22), residues: 1525 helix: 1.90 (0.23), residues: 530 sheet: 0.09 (0.24), residues: 500 loop : -1.69 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 91 TYR 0.011 0.001 TYR B 245 PHE 0.026 0.002 PHE E 247 TRP 0.008 0.001 TRP C 161 HIS 0.003 0.001 HIS E 177 Details of bonding type rmsd covalent geometry : bond 0.00371 (13120) covalent geometry : angle 0.49315 (17830) hydrogen bonds : bond 0.03204 ( 580) hydrogen bonds : angle 3.86959 ( 1845) *********************** 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 132 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.482 Fit side-chains REVERT: A 163 ARG cc_start: 0.8017 (mmt-90) cc_final: 0.7666 (mmp80) REVERT: C 163 ARG cc_start: 0.7927 (mmt-90) cc_final: 0.7519 (mmt-90) REVERT: D 150 GLU cc_start: 0.7751 (pt0) cc_final: 0.7535 (pt0) REVERT: E 174 ARG cc_start: 0.8511 (ttm-80) cc_final: 0.8196 (ttm170) outliers start: 8 outliers final: 7 residues processed: 131 average time/residue: 0.1588 time to fit residues: 28.5093 Evaluate side-chains 118 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 250 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 92 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 119 optimal weight: 20.0000 chunk 98 optimal weight: 3.9990 chunk 88 optimal weight: 0.0670 chunk 123 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 overall best weight: 3.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.143159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.094500 restraints weight = 13449.429| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.16 r_work: 0.2760 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13120 Z= 0.243 Angle : 0.565 5.905 17830 Z= 0.294 Chirality : 0.048 0.157 1955 Planarity : 0.004 0.039 2250 Dihedral : 12.291 104.290 1910 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.65 % Allowed : 9.09 % Favored : 90.25 % 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: 0.19 (0.22), residues: 1525 helix: 1.77 (0.23), residues: 535 sheet: 0.03 (0.23), residues: 500 loop : -1.61 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 99 TYR 0.013 0.001 TYR B 245 PHE 0.023 0.002 PHE E 247 TRP 0.008 0.001 TRP A 206 HIS 0.004 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00621 (13120) covalent geometry : angle 0.56538 (17830) hydrogen bonds : bond 0.03729 ( 580) hydrogen bonds : angle 3.96208 ( 1845) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.489 Fit side-chains REVERT: A 163 ARG cc_start: 0.8019 (mmt-90) cc_final: 0.7613 (mmp80) REVERT: A 245 TYR cc_start: 0.8544 (t80) cc_final: 0.8336 (t80) REVERT: C 156 GLU cc_start: 0.7338 (pm20) cc_final: 0.6856 (mm-30) REVERT: C 163 ARG cc_start: 0.7980 (mmt-90) cc_final: 0.7589 (mmt-90) REVERT: D 150 GLU cc_start: 0.7820 (pt0) cc_final: 0.7565 (pt0) REVERT: E 174 ARG cc_start: 0.8531 (ttm-80) cc_final: 0.8210 (ttm170) outliers start: 9 outliers final: 6 residues processed: 122 average time/residue: 0.1548 time to fit residues: 26.0369 Evaluate side-chains 111 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain E residue 250 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 50 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN E 251 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.147811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.099718 restraints weight = 13300.808| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.13 r_work: 0.2822 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13120 Z= 0.106 Angle : 0.452 4.990 17830 Z= 0.233 Chirality : 0.044 0.136 1955 Planarity : 0.003 0.031 2250 Dihedral : 11.825 104.014 1910 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.87 % Allowed : 9.16 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.22), residues: 1525 helix: 2.13 (0.23), residues: 530 sheet: 0.39 (0.24), residues: 490 loop : -1.55 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 163 TYR 0.011 0.001 TYR E 245 PHE 0.023 0.001 PHE A 247 TRP 0.008 0.001 TRP C 161 HIS 0.003 0.001 HIS E 177 Details of bonding type rmsd covalent geometry : bond 0.00258 (13120) covalent geometry : angle 0.45211 (17830) hydrogen bonds : bond 0.02776 ( 580) hydrogen bonds : angle 3.66114 ( 1845) *********************** 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 144 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.486 Fit side-chains REVERT: A 163 ARG cc_start: 0.7991 (mmt-90) cc_final: 0.7599 (mmp80) REVERT: D 77 GLU cc_start: 0.8679 (tt0) cc_final: 0.8409 (tt0) REVERT: D 150 GLU cc_start: 0.7785 (pt0) cc_final: 0.7559 (pt0) REVERT: E 174 ARG cc_start: 0.8532 (ttm-80) cc_final: 0.8238 (ttm170) outliers start: 12 outliers final: 11 residues processed: 143 average time/residue: 0.1422 time to fit residues: 28.2653 Evaluate side-chains 128 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 279 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 123 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 122 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN C 251 ASN E 251 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.144669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.096554 restraints weight = 13350.483| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.15 r_work: 0.2780 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13120 Z= 0.175 Angle : 0.508 5.254 17830 Z= 0.263 Chirality : 0.046 0.149 1955 Planarity : 0.004 0.034 2250 Dihedral : 11.656 102.856 1910 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.16 % Allowed : 9.45 % Favored : 89.38 % 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: 0.57 (0.22), residues: 1525 helix: 2.05 (0.23), residues: 535 sheet: 0.38 (0.24), residues: 490 loop : -1.48 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 91 TYR 0.014 0.001 TYR E 245 PHE 0.023 0.002 PHE D 247 TRP 0.006 0.001 TRP D 206 HIS 0.003 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00445 (13120) covalent geometry : angle 0.50778 (17830) hydrogen bonds : bond 0.03213 ( 580) hydrogen bonds : angle 3.75136 ( 1845) *********************** 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 134 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.486 Fit side-chains REVERT: A 163 ARG cc_start: 0.8077 (mmt-90) cc_final: 0.7686 (mmp80) REVERT: A 245 TYR cc_start: 0.8473 (t80) cc_final: 0.8210 (t80) REVERT: D 150 GLU cc_start: 0.7842 (pt0) cc_final: 0.7608 (pt0) REVERT: E 174 ARG cc_start: 0.8506 (ttm-80) cc_final: 0.8197 (ttm170) outliers start: 16 outliers final: 15 residues processed: 131 average time/residue: 0.1310 time to fit residues: 24.0963 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 : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 279 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 10 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 chunk 64 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 89 ASN B 251 ASN D 251 ASN E 251 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.148255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.100720 restraints weight = 13158.813| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.06 r_work: 0.2850 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13120 Z= 0.112 Angle : 0.457 4.950 17830 Z= 0.235 Chirality : 0.044 0.137 1955 Planarity : 0.003 0.031 2250 Dihedral : 10.938 102.990 1910 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.80 % Allowed : 9.67 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.22), residues: 1525 helix: 2.23 (0.23), residues: 530 sheet: 0.35 (0.24), residues: 500 loop : -1.34 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 91 TYR 0.011 0.001 TYR E 245 PHE 0.037 0.001 PHE A 247 TRP 0.007 0.001 TRP C 43 HIS 0.003 0.001 HIS E 177 Details of bonding type rmsd covalent geometry : bond 0.00277 (13120) covalent geometry : angle 0.45679 (17830) hydrogen bonds : bond 0.02770 ( 580) hydrogen bonds : angle 3.60605 ( 1845) *********************** 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 128 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.462 Fit side-chains REVERT: A 163 ARG cc_start: 0.8095 (mmt-90) cc_final: 0.7713 (mmp80) REVERT: D 77 GLU cc_start: 0.8719 (tt0) cc_final: 0.8433 (tt0) REVERT: D 150 GLU cc_start: 0.7848 (pt0) cc_final: 0.7637 (pt0) REVERT: E 174 ARG cc_start: 0.8526 (ttm-80) cc_final: 0.8241 (ttm170) outliers start: 11 outliers final: 10 residues processed: 127 average time/residue: 0.1482 time to fit residues: 25.7085 Evaluate side-chains 124 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 279 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 136 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 137 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN D 251 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.143132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.094699 restraints weight = 13426.913| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.17 r_work: 0.2756 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13120 Z= 0.252 Angle : 0.568 5.968 17830 Z= 0.295 Chirality : 0.048 0.156 1955 Planarity : 0.004 0.036 2250 Dihedral : 11.003 100.693 1910 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.87 % Allowed : 9.75 % Favored : 89.38 % 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: 0.48 (0.22), residues: 1525 helix: 1.97 (0.23), residues: 535 sheet: 0.33 (0.24), residues: 490 loop : -1.53 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 163 TYR 0.016 0.002 TYR D 248 PHE 0.029 0.002 PHE A 247 TRP 0.008 0.001 TRP D 206 HIS 0.005 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00645 (13120) covalent geometry : angle 0.56780 (17830) hydrogen bonds : bond 0.03705 ( 580) hydrogen bonds : angle 3.86398 ( 1845) *********************** 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 128 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.475 Fit side-chains REVERT: A 163 ARG cc_start: 0.8076 (mmt-90) cc_final: 0.7692 (mmp80) REVERT: A 245 TYR cc_start: 0.8547 (t80) cc_final: 0.8237 (t80) REVERT: D 150 GLU cc_start: 0.7814 (pt0) cc_final: 0.7594 (pt0) REVERT: E 174 ARG cc_start: 0.8514 (ttm-80) cc_final: 0.8201 (ttm170) outliers start: 12 outliers final: 12 residues processed: 126 average time/residue: 0.1400 time to fit residues: 24.4053 Evaluate side-chains 122 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 157 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 279 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 133 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.147578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.099360 restraints weight = 13242.630| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.15 r_work: 0.2819 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13120 Z= 0.117 Angle : 0.464 4.918 17830 Z= 0.241 Chirality : 0.045 0.137 1955 Planarity : 0.003 0.030 2250 Dihedral : 10.392 100.945 1910 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.87 % Allowed : 9.96 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.22), residues: 1525 helix: 2.19 (0.23), residues: 530 sheet: 0.33 (0.24), residues: 500 loop : -1.33 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 91 TYR 0.013 0.001 TYR E 245 PHE 0.047 0.002 PHE A 247 TRP 0.008 0.001 TRP C 43 HIS 0.003 0.001 HIS E 177 Details of bonding type rmsd covalent geometry : bond 0.00289 (13120) covalent geometry : angle 0.46380 (17830) hydrogen bonds : bond 0.02857 ( 580) hydrogen bonds : angle 3.65112 ( 1845) ********************** 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 127 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.414 Fit side-chains REVERT: A 163 ARG cc_start: 0.8004 (mmt-90) cc_final: 0.7618 (mmp80) REVERT: C 156 GLU cc_start: 0.7115 (pm20) cc_final: 0.6640 (mm-30) REVERT: D 77 GLU cc_start: 0.8727 (tt0) cc_final: 0.8434 (tt0) REVERT: D 150 GLU cc_start: 0.7794 (pt0) cc_final: 0.7579 (pt0) REVERT: E 174 ARG cc_start: 0.8495 (ttm-80) cc_final: 0.8195 (ttm170) outliers start: 12 outliers final: 11 residues processed: 126 average time/residue: 0.1424 time to fit residues: 24.5729 Evaluate side-chains 124 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 157 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 279 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 128 optimal weight: 0.1980 chunk 7 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 147 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 34 optimal weight: 0.4980 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 = 0.3565 r_free = 0.3565 target = 0.145705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.097637 restraints weight = 13353.613| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.15 r_work: 0.2808 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13120 Z= 0.151 Angle : 0.490 5.147 17830 Z= 0.253 Chirality : 0.045 0.145 1955 Planarity : 0.003 0.033 2250 Dihedral : 10.171 100.309 1910 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.80 % Allowed : 10.11 % Favored : 89.09 % 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: 0.69 (0.22), residues: 1525 helix: 2.19 (0.23), residues: 530 sheet: 0.33 (0.24), residues: 500 loop : -1.33 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 163 TYR 0.016 0.001 TYR E 245 PHE 0.049 0.002 PHE A 247 TRP 0.007 0.001 TRP C 43 HIS 0.003 0.001 HIS E 177 Details of bonding type rmsd covalent geometry : bond 0.00384 (13120) covalent geometry : angle 0.48977 (17830) hydrogen bonds : bond 0.03060 ( 580) hydrogen bonds : angle 3.68535 ( 1845) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3342.82 seconds wall clock time: 57 minutes 39.08 seconds (3459.08 seconds total)