Starting phenix.real_space_refine on Fri Jul 3 07:16:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d63_27215/07_2026/8d63_27215.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d63_27215/07_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_27215/07_2026/8d63_27215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d63_27215/07_2026/8d63_27215.map" model { file = "/net/cci-nas-00/data/ceres_data/8d63_27215/07_2026/8d63_27215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d63_27215/07_2026/8d63_27215.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8d63_27215/07_2026/8d63_27215.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d63_27215/07_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-6108/lib/python3.11/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: 2.75, per 1000 atoms: 0.22 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: 0.63 Conformation dependent library (CDL) restraints added in 530.0 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: 0.20 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: 1.46 Time building geometry restraints manager: 0.89 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: 7155 21.58 - 43.15: 420 43.15 - 64.73: 90 64.73 - 86.31: 25 86.31 - 107.88: 15 Dihedral angle restraints: 7705 sinusoidal: 3200 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 7702 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: 0.02 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: 0.490 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.920 Find NCS groups from input model: 0.070 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:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 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 : 15.750 107.881 4795 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/Z covalent geometry : bond 0.00889 / 0.42 (13120) covalent geometry : angle 0.98660 / 0.54 (17830) hydrogen bonds : bond 0.15565 / 10.65 ( 580) hydrogen bonds : angle 6.33847 / 4.42 ( 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 : 0.399 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: 0.1114 time to fit residues: 25.2422 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 : 0.324 ------------------------------------------------------------------------------- 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... 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 = 0.3609 r_free = 0.3609 target = 0.150016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.100952 restraints weight = 13195.070| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.15 r_work: 0.2846 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1289 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= 0.111 Angle : 0.486 5.674 17830 Z= 0.254 Chirality : 0.045 0.134 1955 Planarity : 0.004 0.034 2250 Dihedral : 13.016 112.686 1865 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.44 % Allowed : 4.36 % Favored : 95.20 % 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: -0.07 (0.22), residues: 1525 helix: 1.24 (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 0.011 0.001 TYR B 245 PHE 0.022 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/Z covalent geometry : bond 0.00264 / 0.11 (13120) covalent geometry : angle 0.48594 / 0.25 (17830) hydrogen bonds : bond 0.03299 / 2.17 ( 580) hydrogen bonds : angle 4.19105 / 2.97 ( 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 : 0.338 Fit side-chains REVERT: A 150 GLU cc_start: 0.7795 (pt0) cc_final: 0.7539 (pt0) REVERT: A 163 ARG cc_start: 0.8195 (mmt-90) cc_final: 0.7763 (mmt-90) REVERT: B 60 ASN cc_start: 0.8945 (OUTLIER) cc_final: 0.8643 (m-40) REVERT: B 239 MET cc_start: 0.7451 (ttp) cc_final: 0.6930 (tpp) REVERT: C 163 ARG cc_start: 0.7957 (mmt-90) cc_final: 0.7492 (mmt-90) REVERT: D 150 GLU cc_start: 0.7681 (pt0) cc_final: 0.7418 (pt0) REVERT: E 174 ARG cc_start: 0.8569 (ttm-80) cc_final: 0.8278 (ttm170) outliers start: 6 outliers final: 3 residues processed: 137 average time/residue: 0.1140 time to fit residues: 22.0270 Evaluate side-chains 120 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 116 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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: 10.0000 chunk 83 optimal weight: 4.9990 chunk 58 optimal weight: 30.0000 chunk 17 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3571 r_free = 0.3571 target = 0.146596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.097474 restraints weight = 13340.061| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.16 r_work: 0.2787 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13120 Z= 0.189 Angle : 0.528 5.500 17830 Z= 0.273 Chirality : 0.047 0.143 1955 Planarity : 0.004 0.034 2250 Dihedral : 12.094 109.179 1865 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.65 % Allowed : 6.69 % Favored : 92.65 % 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 (0.22), residues: 1525 helix: 1.63 (0.23), residues: 540 sheet: 0.17 (0.24), residues: 500 loop : -1.60 (0.25), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 99 TYR 0.011 0.001 TYR C 245 PHE 0.016 0.002 PHE E 247 TRP 0.008 0.001 TRP D 206 HIS 0.004 0.001 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.19 (13120) covalent geometry : angle 0.52751 / 0.27 (17830) hydrogen bonds : bond 0.03520 / 2.32 ( 580) hydrogen bonds : angle 4.00717 / 2.84 ( 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 131 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.460 Fit side-chains REVERT: A 163 ARG cc_start: 0.8100 (mmt-90) cc_final: 0.7689 (mmt-90) REVERT: B 60 ASN cc_start: 0.8999 (OUTLIER) cc_final: 0.8732 (m-40) REVERT: C 156 GLU cc_start: 0.7334 (pm20) cc_final: 0.6834 (mm-30) REVERT: C 163 ARG cc_start: 0.7962 (mmt-90) cc_final: 0.7546 (mmt-90) REVERT: D 150 GLU cc_start: 0.7784 (pt0) cc_final: 0.7562 (pt0) REVERT: D 155 GLU cc_start: 0.6775 (pt0) cc_final: 0.6548 (pt0) REVERT: E 174 ARG cc_start: 0.8546 (ttm-80) cc_final: 0.8230 (ttm170) outliers start: 9 outliers final: 7 residues processed: 129 average time/residue: 0.1187 time to fit residues: 21.2394 Evaluate side-chains 116 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN 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 D residue 279 LEU Chi-restraints excluded: chain E residue 60 ASN 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: 0.4980 chunk 33 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 8 optimal weight: 0.1980 chunk 1 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 60 ASN B 251 ASN C 60 ASN E 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.145924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.097075 restraints weight = 13324.564| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.16 r_work: 0.2787 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1630 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= 0.175 Angle : 0.506 5.265 17830 Z= 0.262 Chirality : 0.046 0.143 1955 Planarity : 0.004 0.032 2250 Dihedral : 11.017 107.130 1865 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.65 % Allowed : 7.27 % Favored : 92.07 % 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: 1.85 (0.23), residues: 540 sheet: 0.17 (0.24), residues: 500 loop : -1.50 (0.25), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 199 TYR 0.011 0.001 TYR B 245 PHE 0.022 0.002 PHE E 247 TRP 0.007 0.001 TRP D 206 HIS 0.003 0.001 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.17 (13120) covalent geometry : angle 0.50606 / 0.26 (17830) hydrogen bonds : bond 0.03329 / 2.19 ( 580) hydrogen bonds : angle 3.88125 / 2.75 ( 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 127 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.329 Fit side-chains REVERT: A 150 GLU cc_start: 0.7943 (pt0) cc_final: 0.7658 (pt0) REVERT: A 163 ARG cc_start: 0.8075 (mmt-90) cc_final: 0.7681 (mmt-90) REVERT: D 77 GLU cc_start: 0.8753 (tt0) cc_final: 0.8494 (tt0) REVERT: E 174 ARG cc_start: 0.8546 (ttm-80) cc_final: 0.8214 (ttm170) outliers start: 9 outliers final: 7 residues processed: 125 average time/residue: 0.1232 time to fit residues: 21.0361 Evaluate side-chains 114 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN 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=3.50 ------------------------------------------------------------------------------- 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: 5.9990 chunk 108 optimal weight: 0.8980 chunk 119 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 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 = 0.3544 r_free = 0.3544 target = 0.144091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.095209 restraints weight = 13389.381| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.16 r_work: 0.2753 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1807 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= 0.242 Angle : 0.562 5.742 17830 Z= 0.293 Chirality : 0.048 0.156 1955 Planarity : 0.004 0.038 2250 Dihedral : 10.821 102.972 1865 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.87 % Allowed : 8.51 % Favored : 90.62 % 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: 0.30 (0.22), residues: 1525 helix: 1.81 (0.23), residues: 535 sheet: 0.22 (0.24), residues: 490 loop : -1.61 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 141 TYR 0.014 0.002 TYR A 248 PHE 0.019 0.002 PHE D 247 TRP 0.008 0.001 TRP D 206 HIS 0.004 0.001 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.24 (13120) covalent geometry : angle 0.56186 / 0.29 (17830) hydrogen bonds : bond 0.03738 / 2.45 ( 580) hydrogen bonds : angle 3.96934 / 2.81 ( 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 132 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.491 Fit side-chains REVERT: A 163 ARG cc_start: 0.8120 (mmt-90) cc_final: 0.7772 (mmt-90) REVERT: A 245 TYR cc_start: 0.8530 (t80) cc_final: 0.8258 (t80) REVERT: D 150 GLU cc_start: 0.7792 (pt0) cc_final: 0.7245 (mt-10) REVERT: D 155 GLU cc_start: 0.6766 (pt0) cc_final: 0.6516 (pt0) REVERT: E 174 ARG cc_start: 0.8544 (ttm-80) cc_final: 0.8223 (ttm170) outliers start: 12 outliers final: 10 residues processed: 129 average time/residue: 0.1271 time to fit residues: 22.6421 Evaluate side-chains 117 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 50 optimal weight: 0.1980 chunk 144 optimal weight: 1.9990 chunk 88 optimal weight: 30.0000 chunk 96 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 251 ASN D 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 = 0.3592 r_free = 0.3592 target = 0.148453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.099881 restraints weight = 13301.345| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.18 r_work: 0.2827 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13120 Z= 0.102 Angle : 0.444 4.919 17830 Z= 0.230 Chirality : 0.044 0.134 1955 Planarity : 0.003 0.030 2250 Dihedral : 10.216 101.954 1865 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.87 % Allowed : 8.87 % 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: 0.66 (0.22), residues: 1525 helix: 2.23 (0.23), residues: 525 sheet: 0.42 (0.24), residues: 490 loop : -1.49 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 91 TYR 0.011 0.001 TYR E 245 PHE 0.024 0.001 PHE D 247 TRP 0.007 0.001 TRP E 43 HIS 0.002 0.001 HIS E 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.10 (13120) covalent geometry : angle 0.44439 / 0.23 (17830) hydrogen bonds : bond 0.02741 / 1.81 ( 580) hydrogen bonds : angle 3.66011 / 2.61 ( 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 137 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.290 Fit side-chains REVERT: D 150 GLU cc_start: 0.7748 (pt0) cc_final: 0.7207 (mt-10) REVERT: E 163 ARG cc_start: 0.7941 (mmt180) cc_final: 0.7658 (mmt180) REVERT: E 174 ARG cc_start: 0.8506 (ttm-80) cc_final: 0.8205 (ttm170) outliers start: 12 outliers final: 10 residues processed: 136 average time/residue: 0.1091 time to fit residues: 20.5025 Evaluate side-chains 128 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 D residue 250 SER Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 250 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 123 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 111 optimal weight: 0.0670 chunk 99 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 overall best weight: 2.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 251 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.145101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.096747 restraints weight = 13354.469| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.16 r_work: 0.2785 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13120 Z= 0.176 Angle : 0.498 5.263 17830 Z= 0.258 Chirality : 0.046 0.145 1955 Planarity : 0.004 0.033 2250 Dihedral : 10.144 100.426 1865 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.73 % Allowed : 9.38 % 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: 0.61 (0.22), residues: 1525 helix: 2.13 (0.23), residues: 530 sheet: 0.39 (0.24), residues: 490 loop : -1.48 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 91 TYR 0.010 0.001 TYR D 245 PHE 0.023 0.002 PHE D 247 TRP 0.006 0.001 TRP C 206 HIS 0.003 0.001 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.18 (13120) covalent geometry : angle 0.49809 / 0.26 (17830) hydrogen bonds : bond 0.03177 / 2.09 ( 580) hydrogen bonds : angle 3.74764 / 2.66 ( 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 131 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.474 Fit side-chains REVERT: A 245 TYR cc_start: 0.8491 (t80) cc_final: 0.8270 (t80) REVERT: D 150 GLU cc_start: 0.7817 (pt0) cc_final: 0.7274 (mt-10) REVERT: E 174 ARG cc_start: 0.8504 (ttm-80) cc_final: 0.8194 (ttm170) outliers start: 10 outliers final: 10 residues processed: 129 average time/residue: 0.1210 time to fit residues: 22.0587 Evaluate side-chains 121 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 191 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 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: 1.9990 chunk 9 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 148 optimal weight: 20.0000 chunk 64 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 251 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.147407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.098982 restraints weight = 13212.455| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.17 r_work: 0.2812 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2050 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= 0.126 Angle : 0.464 4.981 17830 Z= 0.240 Chirality : 0.045 0.137 1955 Planarity : 0.003 0.031 2250 Dihedral : 9.872 99.391 1865 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.73 % Allowed : 9.75 % 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: 0.71 (0.22), residues: 1525 helix: 2.20 (0.23), residues: 530 sheet: 0.33 (0.24), residues: 500 loop : -1.30 (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 A 248 PHE 0.041 0.002 PHE A 247 TRP 0.007 0.001 TRP C 43 HIS 0.002 0.001 HIS D 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (13120) covalent geometry : angle 0.46381 / 0.24 (17830) hydrogen bonds : bond 0.02881 / 1.90 ( 580) hydrogen bonds : angle 3.64187 / 2.59 ( 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 126 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.474 Fit side-chains REVERT: D 150 GLU cc_start: 0.7784 (pt0) cc_final: 0.7232 (mt-10) REVERT: E 163 ARG cc_start: 0.7845 (mmt180) cc_final: 0.7522 (mmt180) REVERT: E 174 ARG cc_start: 0.8499 (ttm-80) cc_final: 0.8199 (ttm170) outliers start: 10 outliers final: 9 residues processed: 124 average time/residue: 0.1237 time to fit residues: 21.1153 Evaluate side-chains 121 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 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 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: 5.9990 chunk 82 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 135 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 251 ASN B 251 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.143000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.094351 restraints weight = 13461.592| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.18 r_work: 0.2749 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 13120 Z= 0.284 Angle : 0.587 6.209 17830 Z= 0.306 Chirality : 0.049 0.163 1955 Planarity : 0.004 0.037 2250 Dihedral : 10.232 97.205 1865 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.65 % Allowed : 9.82 % 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: 0.42 (0.22), residues: 1525 helix: 1.88 (0.23), residues: 535 sheet: 0.29 (0.24), residues: 490 loop : -1.52 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 141 TYR 0.020 0.002 TYR D 248 PHE 0.041 0.002 PHE A 247 TRP 0.009 0.001 TRP C 206 HIS 0.005 0.002 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00728 / 0.28 (13120) covalent geometry : angle 0.58744 / 0.31 (17830) hydrogen bonds : bond 0.03885 / 2.54 ( 580) hydrogen bonds : angle 3.90653 / 2.76 ( 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 122 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.323 Fit side-chains REVERT: A 163 ARG cc_start: 0.7958 (mmt-90) cc_final: 0.7653 (mmp80) REVERT: A 245 TYR cc_start: 0.8605 (t80) cc_final: 0.8298 (t80) REVERT: D 150 GLU cc_start: 0.7812 (pt0) cc_final: 0.7248 (mt-10) REVERT: E 174 ARG cc_start: 0.8525 (ttm-80) cc_final: 0.8207 (ttm170) outliers start: 9 outliers final: 9 residues processed: 120 average time/residue: 0.1216 time to fit residues: 20.1833 Evaluate side-chains 117 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 191 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 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: 0.7980 chunk 85 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 251 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.146399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.098189 restraints weight = 13269.909| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.16 r_work: 0.2821 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13120 Z= 0.141 Angle : 0.481 5.058 17830 Z= 0.251 Chirality : 0.045 0.142 1955 Planarity : 0.003 0.031 2250 Dihedral : 9.867 96.246 1865 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.58 % Allowed : 10.04 % 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: 2.11 (0.23), residues: 530 sheet: 0.23 (0.24), residues: 500 loop : -1.37 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 91 TYR 0.016 0.001 TYR A 248 PHE 0.050 0.002 PHE A 247 TRP 0.007 0.001 TRP C 43 HIS 0.003 0.001 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.14 (13120) covalent geometry : angle 0.48132 / 0.25 (17830) hydrogen bonds : bond 0.03036 / 2.00 ( 580) hydrogen bonds : angle 3.69931 / 2.63 ( 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 125 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.357 Fit side-chains REVERT: A 163 ARG cc_start: 0.7975 (mmt-90) cc_final: 0.7662 (mmp80) REVERT: A 245 TYR cc_start: 0.8477 (t80) cc_final: 0.8250 (t80) REVERT: D 150 GLU cc_start: 0.7765 (pt0) cc_final: 0.7222 (mt-10) REVERT: E 174 ARG cc_start: 0.8514 (ttm-80) cc_final: 0.8212 (ttm170) outliers start: 8 outliers final: 8 residues processed: 124 average time/residue: 0.1238 time to fit residues: 21.1181 Evaluate side-chains 117 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 191 ILE Chi-restraints excluded: chain D residue 250 SER 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: 0.0870 chunk 7 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 147 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 overall best weight: 2.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 251 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.144809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.096408 restraints weight = 13391.687| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.18 r_work: 0.2808 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13120 Z= 0.190 Angle : 0.518 5.214 17830 Z= 0.270 Chirality : 0.047 0.147 1955 Planarity : 0.004 0.034 2250 Dihedral : 9.814 95.443 1865 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.65 % Allowed : 10.04 % Favored : 89.31 % 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: 0.57 (0.22), residues: 1525 helix: 2.02 (0.23), residues: 535 sheet: 0.36 (0.24), residues: 490 loop : -1.42 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 163 TYR 0.018 0.001 TYR D 248 PHE 0.048 0.002 PHE A 247 TRP 0.008 0.001 TRP C 206 HIS 0.004 0.001 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.19 (13120) covalent geometry : angle 0.51822 / 0.27 (17830) hydrogen bonds : bond 0.03343 / 2.20 ( 580) hydrogen bonds : angle 3.76588 / 2.67 ( 1845) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2812.51 seconds wall clock time: 48 minutes 35.64 seconds (2915.64 seconds total)