Starting phenix.real_space_refine on Fri Jul 3 07:31:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ngg_49384/07_2026/9ngg_49384_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ngg_49384/07_2026/9ngg_49384.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ngg_49384/07_2026/9ngg_49384_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ngg_49384/07_2026/9ngg_49384_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ngg_49384/07_2026/9ngg_49384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ngg_49384/07_2026/9ngg_49384.map" } resolution = 3.6 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= 0.005 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 S 30 5.16 5 Na 7 4.78 5 C 8230 2.51 5 N 2090 2.21 5 O 2260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 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: 12617 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2522 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Conformer: "B" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} bond proxies already assigned to first conformer: 2553 Chain: "B" Number of atoms: 2522 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Conformer: "B" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} bond proxies already assigned to first conformer: 2553 Chain: "C" Number of atoms: 2522 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Conformer: "B" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} bond proxies already assigned to first conformer: 2553 Chain: "D" Number of atoms: 2522 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Conformer: "B" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} bond proxies already assigned to first conformer: 2553 Chain: "E" Number of atoms: 2522 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Conformer: "B" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} bond proxies already assigned to first conformer: 2553 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 0 Ad-hoc single atom residues: {' NA': 5} Chain breaks: 5 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' NA': 1} Chain breaks: 1 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' NA': 1} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N APHE A 247 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 247 " occ=0.50 residue: pdb=" N APHE B 247 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 247 " occ=0.50 residue: pdb=" N APHE C 247 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 247 " occ=0.50 residue: pdb=" N APHE D 247 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 247 " occ=0.50 residue: pdb=" N APHE E 247 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE E 247 " occ=0.50 Time building chain proxies: 4.99, per 1000 atoms: 0.40 Number of scatterers: 12617 At special positions: 0 Unit cell: (91.14, 91.14, 123.256, 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 Na 7 11.00 O 2260 8.00 N 2090 7.00 C 8230 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: 0.98 Conformation dependent library (CDL) restraints added in 995.2 milliseconds 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2930 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 20 sheets defined 38.8% alpha, 39.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 62 through 70 removed outlier: 3.745A pdb=" N TRP A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.535A pdb=" N SER A 179 " --> pdb=" O ASP A 176 " (cutoff:3.500A) removed outlier: 3.930A 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 221 Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 227 through 253 removed outlier: 3.611A pdb=" N ASN A 251 " --> pdb=" O BPHE A 247 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 285 Processing helix chain 'A' and resid 296 through 302 removed outlier: 3.687A pdb=" N ARG A 299 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS A 300 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG A 301 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU A 302 " --> pdb=" O ARG A 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 296 through 302' Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'B' and resid 62 through 70 removed outlier: 3.745A pdb=" N TRP B 66 " --> pdb=" O GLN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'B' and resid 176 through 180 removed outlier: 3.534A pdb=" N SER B 179 " --> pdb=" O ASP B 176 " (cutoff:3.500A) removed outlier: 3.929A 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 221 Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 227 through 253 removed outlier: 3.612A pdb=" N ASN B 251 " --> pdb=" O BPHE B 247 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 285 Processing helix chain 'B' and resid 296 through 302 removed outlier: 3.687A pdb=" N ARG B 299 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS B 300 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG B 301 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU B 302 " --> pdb=" O ARG B 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 296 through 302' Processing helix chain 'B' and resid 303 through 317 Processing helix chain 'C' and resid 62 through 70 removed outlier: 3.746A pdb=" N TRP C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'C' and resid 176 through 180 removed outlier: 3.535A pdb=" N SER C 179 " --> pdb=" O ASP C 176 " (cutoff:3.500A) removed outlier: 3.929A 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 221 Processing helix chain 'C' and resid 222 through 225 Processing helix chain 'C' and resid 227 through 253 removed outlier: 3.612A pdb=" N ASN C 251 " --> pdb=" O BPHE C 247 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 285 Processing helix chain 'C' and resid 296 through 302 removed outlier: 3.686A pdb=" N ARG C 299 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N CYS C 300 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG C 301 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU C 302 " --> pdb=" O ARG C 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 296 through 302' Processing helix chain 'C' and resid 303 through 317 Processing helix chain 'D' and resid 62 through 70 removed outlier: 3.745A pdb=" N TRP D 66 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 121 Processing helix chain 'D' and resid 176 through 180 removed outlier: 3.534A pdb=" N SER D 179 " --> pdb=" O ASP D 176 " (cutoff:3.500A) removed outlier: 3.930A 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 221 Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 227 through 253 removed outlier: 3.611A pdb=" N ASN D 251 " --> pdb=" O BPHE D 247 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE D 252 " --> pdb=" O TYR D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 285 Processing helix chain 'D' and resid 296 through 302 removed outlier: 3.687A pdb=" N ARG D 299 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS D 300 " --> pdb=" O ILE D 297 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG D 301 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU D 302 " --> pdb=" O ARG D 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 296 through 302' Processing helix chain 'D' and resid 303 through 317 Processing helix chain 'E' and resid 62 through 70 removed outlier: 3.745A pdb=" N TRP E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 121 Processing helix chain 'E' and resid 176 through 180 removed outlier: 3.534A pdb=" N SER E 179 " --> pdb=" O ASP E 176 " (cutoff:3.500A) removed outlier: 3.930A 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 221 Processing helix chain 'E' and resid 222 through 225 Processing helix chain 'E' and resid 227 through 253 removed outlier: 3.611A pdb=" N ASN E 251 " --> pdb=" O BPHE E 247 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE E 252 " --> pdb=" O TYR E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 285 Processing helix chain 'E' and resid 296 through 302 removed outlier: 3.687A pdb=" N ARG E 299 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS E 300 " --> pdb=" O ILE E 297 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG E 301 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU E 302 " --> pdb=" O ARG E 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 296 through 302' Processing helix chain 'E' and resid 303 through 317 Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 27 removed outlier: 3.677A pdb=" N LYS A 22 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL A 26 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR A 32 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 108 " --> pdb=" O VAL A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 27 removed outlier: 3.677A pdb=" N LYS A 22 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL A 26 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR A 32 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR A 44 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ASP A 13 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL A 14 " --> pdb=" O ASP A 144 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N GLN A 146 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N VAL A 16 " --> pdb=" O GLN A 146 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N TYR A 148 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE A 18 " --> pdb=" O TYR A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.874A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.874A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 22 through 27 removed outlier: 3.677A pdb=" N LYS B 22 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL B 26 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR B 32 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY B 108 " --> pdb=" O VAL B 35 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 22 through 27 removed outlier: 3.677A pdb=" N LYS B 22 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL B 26 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR B 32 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR B 44 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ASP B 13 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL B 14 " --> pdb=" O ASP B 144 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N GLN B 146 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N VAL B 16 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N TYR B 148 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE B 18 " --> pdb=" O TYR B 148 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.875A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.875A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 22 through 27 removed outlier: 3.677A pdb=" N LYS C 22 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL C 26 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY C 108 " --> pdb=" O VAL C 35 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 22 through 27 removed outlier: 3.677A pdb=" N LYS C 22 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL C 26 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR C 44 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASP C 13 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL C 14 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N GLN C 146 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N VAL C 16 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N TYR C 148 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE C 18 " --> pdb=" O TYR C 148 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.874A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.874A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 22 through 27 removed outlier: 3.676A pdb=" N LYS D 22 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL D 26 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR D 32 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY D 108 " --> pdb=" O VAL D 35 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 22 through 27 removed outlier: 3.676A pdb=" N LYS D 22 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL D 26 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR D 32 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR D 44 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASP D 13 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL D 14 " --> pdb=" O ASP D 144 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N GLN D 146 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N VAL D 16 " --> pdb=" O GLN D 146 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N TYR D 148 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE D 18 " --> pdb=" O TYR D 148 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.874A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.874A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 22 through 27 removed outlier: 3.676A pdb=" N LYS E 22 " --> pdb=" O ASP E 36 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL E 26 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR E 32 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY E 108 " --> pdb=" O VAL E 35 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 22 through 27 removed outlier: 3.676A pdb=" N LYS E 22 " --> pdb=" O ASP E 36 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL E 26 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR E 32 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR E 44 " --> pdb=" O ASP E 13 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ASP E 13 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL E 14 " --> pdb=" O ASP E 144 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N GLN E 146 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N VAL E 16 " --> pdb=" O GLN E 146 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N TYR E 148 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE E 18 " --> pdb=" O TYR E 148 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.873A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.873A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) 685 hydrogen bonds defined for protein. 1995 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: 2.16 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4005 1.34 - 1.46: 2901 1.46 - 1.58: 6009 1.58 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 12965 Sorted by residual: bond pdb=" N THR E 61 " pdb=" CA THR E 61 " ideal model delta sigma weight residual 1.462 1.482 -0.020 1.48e-02 4.57e+03 1.80e+00 bond pdb=" N THR C 61 " pdb=" CA THR C 61 " ideal model delta sigma weight residual 1.462 1.481 -0.020 1.48e-02 4.57e+03 1.77e+00 bond pdb=" N THR A 61 " pdb=" CA THR A 61 " ideal model delta sigma weight residual 1.462 1.481 -0.020 1.48e-02 4.57e+03 1.75e+00 bond pdb=" N THR D 61 " pdb=" CA THR D 61 " ideal model delta sigma weight residual 1.462 1.481 -0.019 1.48e-02 4.57e+03 1.73e+00 bond pdb=" N THR B 61 " pdb=" CA THR B 61 " ideal model delta sigma weight residual 1.462 1.481 -0.019 1.48e-02 4.57e+03 1.61e+00 ... (remaining 12960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 17312 1.74 - 3.48: 303 3.48 - 5.22: 35 5.22 - 6.97: 30 6.97 - 8.71: 5 Bond angle restraints: 17685 Sorted by residual: angle pdb=" C ASN B 60 " pdb=" N THR B 61 " pdb=" CA THR B 61 " ideal model delta sigma weight residual 122.61 128.09 -5.48 1.56e+00 4.11e-01 1.24e+01 angle pdb=" C ASN A 60 " pdb=" N THR A 61 " pdb=" CA THR A 61 " ideal model delta sigma weight residual 122.61 128.06 -5.45 1.56e+00 4.11e-01 1.22e+01 angle pdb=" C ASN E 60 " pdb=" N THR E 61 " pdb=" CA THR E 61 " ideal model delta sigma weight residual 122.61 128.03 -5.42 1.56e+00 4.11e-01 1.21e+01 angle pdb=" C ASN C 60 " pdb=" N THR C 61 " pdb=" CA THR C 61 " ideal model delta sigma weight residual 122.61 128.03 -5.42 1.56e+00 4.11e-01 1.21e+01 angle pdb=" C ASN D 60 " pdb=" N THR D 61 " pdb=" CA THR D 61 " ideal model delta sigma weight residual 122.61 128.01 -5.40 1.56e+00 4.11e-01 1.20e+01 ... (remaining 17680 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 6835 17.93 - 35.86: 626 35.86 - 53.79: 89 53.79 - 71.73: 20 71.73 - 89.66: 20 Dihedral angle restraints: 7590 sinusoidal: 3045 harmonic: 4545 Sorted by residual: dihedral pdb=" CB GLU B 156 " pdb=" CG GLU B 156 " pdb=" CD GLU B 156 " pdb=" OE1 GLU B 156 " ideal model delta sinusoidal sigma weight residual 0.00 89.66 -89.66 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU D 156 " pdb=" CG GLU D 156 " pdb=" CD GLU D 156 " pdb=" OE1 GLU D 156 " ideal model delta sinusoidal sigma weight residual 0.00 89.63 -89.63 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU C 156 " pdb=" CG GLU C 156 " pdb=" CD GLU C 156 " pdb=" OE1 GLU C 156 " ideal model delta sinusoidal sigma weight residual 0.00 89.61 -89.61 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 7587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1332 0.042 - 0.085: 412 0.085 - 0.127: 182 0.127 - 0.169: 24 0.169 - 0.211: 10 Chirality restraints: 1960 Sorted by residual: chirality pdb=" CB THR B 149 " pdb=" CA THR B 149 " pdb=" OG1 THR B 149 " pdb=" CG2 THR B 149 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CB THR D 149 " pdb=" CA THR D 149 " pdb=" OG1 THR D 149 " pdb=" CG2 THR D 149 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CB THR C 149 " pdb=" CA THR C 149 " pdb=" OG1 THR C 149 " pdb=" CG2 THR C 149 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1957 not shown) Planarity restraints: 2260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB BPHE D 247 " -0.015 2.00e-02 2.50e+03 1.60e-02 4.47e+00 pdb=" CG BPHE D 247 " 0.037 2.00e-02 2.50e+03 pdb=" CD1BPHE D 247 " -0.010 2.00e-02 2.50e+03 pdb=" CD2BPHE D 247 " -0.006 2.00e-02 2.50e+03 pdb=" CE1BPHE D 247 " -0.002 2.00e-02 2.50e+03 pdb=" CE2BPHE D 247 " -0.005 2.00e-02 2.50e+03 pdb=" CZ BPHE D 247 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BPHE C 247 " 0.015 2.00e-02 2.50e+03 1.59e-02 4.40e+00 pdb=" CG BPHE C 247 " -0.037 2.00e-02 2.50e+03 pdb=" CD1BPHE C 247 " 0.010 2.00e-02 2.50e+03 pdb=" CD2BPHE C 247 " 0.006 2.00e-02 2.50e+03 pdb=" CE1BPHE C 247 " 0.002 2.00e-02 2.50e+03 pdb=" CE2BPHE C 247 " 0.005 2.00e-02 2.50e+03 pdb=" CZ BPHE C 247 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BPHE E 247 " -0.015 2.00e-02 2.50e+03 1.58e-02 4.40e+00 pdb=" CG BPHE E 247 " 0.037 2.00e-02 2.50e+03 pdb=" CD1BPHE E 247 " -0.010 2.00e-02 2.50e+03 pdb=" CD2BPHE E 247 " -0.006 2.00e-02 2.50e+03 pdb=" CE1BPHE E 247 " -0.002 2.00e-02 2.50e+03 pdb=" CE2BPHE E 247 " -0.005 2.00e-02 2.50e+03 pdb=" CZ BPHE E 247 " 0.001 2.00e-02 2.50e+03 ... (remaining 2257 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 207 2.70 - 3.25: 11542 3.25 - 3.80: 19550 3.80 - 4.35: 24645 4.35 - 4.90: 43573 Nonbonded interactions: 99517 Sorted by model distance: nonbonded pdb=" CB SER A 229 " pdb=" OE2 GLU B 230 " model vdw 2.155 3.440 nonbonded pdb=" CB SER C 229 " pdb=" OE2 GLU D 230 " model vdw 2.181 3.440 nonbonded pdb=" CB SER D 229 " pdb=" OE2 GLU E 230 " model vdw 2.196 3.440 nonbonded pdb=" CB SER B 229 " pdb=" OE2 GLU C 230 " model vdw 2.214 3.440 nonbonded pdb=" OE2 GLU A 230 " pdb=" CB SER E 229 " model vdw 2.247 3.440 ... (remaining 99512 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 232 or resid 234 through 246 or resid 248 throu \ gh 317)) selection = (chain 'B' and (resid 11 through 232 or resid 234 through 246 or resid 248 throu \ gh 317)) selection = (chain 'C' and (resid 11 through 232 or resid 234 through 246 or resid 248 throu \ gh 317)) selection = (chain 'D' and (resid 11 through 232 or resid 234 through 246 or resid 248 throu \ gh 317)) selection = (chain 'E' and (resid 11 through 232 or resid 234 through 246 or resid 248 throu \ gh 317)) } 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=0.30 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.380 Find NCS groups from input model: 0.300 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 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 : 0.003 0.029 12965 Z= 0.146 Angle : 0.641 8.707 17685 Z= 0.338 Chirality : 0.051 0.211 1960 Planarity : 0.005 0.036 2260 Dihedral : 14.563 89.657 4660 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: 1545 helix: 0.58 (0.21), residues: 550 sheet: 1.42 (0.26), residues: 480 loop : -1.94 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 255 TYR 0.011 0.001 TYR C 270 PHE 0.010 0.001 PHE E 236 TRP 0.009 0.001 TRP E 206 HIS 0.006 0.002 HIS B 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 (12965) covalent geometry : angle 0.64076 / 0.34 (17685) hydrogen bonds : bond 0.18437 / 12.17 ( 620) hydrogen bonds : angle 6.82272 / 4.77 ( 1995) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.355 Fit side-chains REVERT: C 90 LYS cc_start: 0.7883 (mtmm) cc_final: 0.7622 (mtmm) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.0781 time to fit residues: 21.3568 Evaluate side-chains 155 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 0.1980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 284 HIS B 284 HIS C 124 GLN C 284 HIS D 124 GLN D 284 HIS E 124 GLN E 284 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.161881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.142887 restraints weight = 33590.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.145828 restraints weight = 20324.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.147798 restraints weight = 12615.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.150958 restraints weight = 8506.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.151377 restraints weight = 6435.636| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12965 Z= 0.116 Angle : 0.519 5.990 17685 Z= 0.273 Chirality : 0.046 0.152 1960 Planarity : 0.004 0.031 2260 Dihedral : 4.081 14.671 1705 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.83 (0.22), residues: 1545 helix: 1.79 (0.22), residues: 550 sheet: 1.52 (0.25), residues: 480 loop : -1.89 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 91 TYR 0.008 0.001 TYR B 245 PHE 0.013 0.001 PHE D 95 TRP 0.009 0.001 TRP A 43 HIS 0.006 0.002 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (12965) covalent geometry : angle 0.51856 / 0.27 (17685) hydrogen bonds : bond 0.03914 / 2.56 ( 620) hydrogen bonds : angle 4.56079 / 3.16 ( 1995) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.345 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.0832 time to fit residues: 18.7721 Evaluate side-chains 127 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 124 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 84 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 119 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.159201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.138776 restraints weight = 40573.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.142774 restraints weight = 28061.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.144395 restraints weight = 14402.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.147525 restraints weight = 10003.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.147820 restraints weight = 7550.298| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12965 Z= 0.117 Angle : 0.503 5.954 17685 Z= 0.263 Chirality : 0.046 0.147 1960 Planarity : 0.004 0.027 2260 Dihedral : 3.983 14.802 1705 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.22 % Allowed : 8.81 % Favored : 90.97 % 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: 1.07 (0.22), residues: 1545 helix: 2.20 (0.22), residues: 560 sheet: 1.31 (0.25), residues: 490 loop : -1.80 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 255 TYR 0.008 0.001 TYR B 245 PHE 0.010 0.001 PHE A 95 TRP 0.008 0.001 TRP A 43 HIS 0.005 0.001 HIS C 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (12965) covalent geometry : angle 0.50291 / 0.26 (17685) hydrogen bonds : bond 0.03758 / 2.45 ( 620) hydrogen bonds : angle 4.16404 / 2.88 ( 1995) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 140 time to evaluate : 0.360 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 141 average time/residue: 0.0879 time to fit residues: 19.8626 Evaluate side-chains 135 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 195 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 136 optimal weight: 3.9990 chunk 93 optimal weight: 0.0870 chunk 55 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.156186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.137014 restraints weight = 38386.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.139488 restraints weight = 29309.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.140756 restraints weight = 16483.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.143867 restraints weight = 12771.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.144007 restraints weight = 8574.269| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 12965 Z= 0.114 Angle : 0.500 6.787 17685 Z= 0.259 Chirality : 0.045 0.146 1960 Planarity : 0.003 0.027 2260 Dihedral : 3.980 14.598 1705 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.14 % Allowed : 9.31 % Favored : 90.54 % 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: 1.15 (0.23), residues: 1545 helix: 2.38 (0.22), residues: 560 sheet: 1.31 (0.26), residues: 470 loop : -1.73 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 255 TYR 0.009 0.001 TYR B 175 PHE 0.009 0.001 PHE C 236 TRP 0.008 0.001 TRP D 43 HIS 0.004 0.001 HIS D 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (12965) covalent geometry : angle 0.49992 / 0.26 (17685) hydrogen bonds : bond 0.03576 / 2.33 ( 620) hydrogen bonds : angle 4.08286 / 2.82 ( 1995) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 143 time to evaluate : 0.479 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 144 average time/residue: 0.0852 time to fit residues: 19.5400 Evaluate side-chains 138 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 195 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 122 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 93 optimal weight: 0.0670 chunk 3 optimal weight: 0.0270 overall best weight: 1.1380 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.179676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.153935 restraints weight = 33192.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.159983 restraints weight = 15554.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.164331 restraints weight = 9178.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.167089 restraints weight = 6220.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.168069 restraints weight = 4772.720| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 12965 Z= 0.122 Angle : 0.503 6.826 17685 Z= 0.261 Chirality : 0.046 0.146 1960 Planarity : 0.003 0.027 2260 Dihedral : 4.012 14.401 1705 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.22 % Allowed : 9.89 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.23), residues: 1545 helix: 2.44 (0.23), residues: 560 sheet: 1.25 (0.26), residues: 470 loop : -1.69 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 255 TYR 0.009 0.001 TYR E 245 PHE 0.009 0.001 PHE B 236 TRP 0.007 0.001 TRP A 43 HIS 0.005 0.001 HIS D 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (12965) covalent geometry : angle 0.50275 / 0.26 (17685) hydrogen bonds : bond 0.03642 / 2.37 ( 620) hydrogen bonds : angle 4.05969 / 2.80 ( 1995) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 149 time to evaluate : 0.485 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 150 average time/residue: 0.0939 time to fit residues: 21.0990 Evaluate side-chains 147 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain D residue 195 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 72 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 17 optimal weight: 0.0060 chunk 43 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 149 optimal weight: 0.0050 overall best weight: 0.7412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.157237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.139765 restraints weight = 47752.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.141488 restraints weight = 45200.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.142475 restraints weight = 18128.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.144015 restraints weight = 11878.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.144080 restraints weight = 9559.124| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 12965 Z= 0.101 Angle : 0.484 7.195 17685 Z= 0.250 Chirality : 0.045 0.142 1960 Planarity : 0.003 0.029 2260 Dihedral : 3.872 13.376 1705 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.14 % Allowed : 10.54 % 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: 1.21 (0.23), residues: 1545 helix: 2.47 (0.22), residues: 560 sheet: 1.23 (0.26), residues: 470 loop : -1.64 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 255 TYR 0.009 0.001 TYR B 245 PHE 0.007 0.001 PHE D 95 TRP 0.007 0.001 TRP B 43 HIS 0.004 0.001 HIS D 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (12965) covalent geometry : angle 0.48398 / 0.25 (17685) hydrogen bonds : bond 0.03300 / 2.15 ( 620) hydrogen bonds : angle 3.96416 / 2.74 ( 1995) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 143 time to evaluate : 0.474 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 143 average time/residue: 0.1060 time to fit residues: 23.1124 Evaluate side-chains 141 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 139 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain B residue 63 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 113 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.154382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.135524 restraints weight = 33842.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.138431 restraints weight = 25351.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.140217 restraints weight = 15125.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.141541 restraints weight = 10475.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.141999 restraints weight = 9051.151| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 12965 Z= 0.122 Angle : 0.499 7.080 17685 Z= 0.259 Chirality : 0.045 0.144 1960 Planarity : 0.003 0.032 2260 Dihedral : 3.977 13.800 1705 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.29 % Allowed : 11.05 % Favored : 88.66 % 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: 1.20 (0.23), residues: 1545 helix: 2.47 (0.22), residues: 560 sheet: 1.27 (0.27), residues: 455 loop : -1.60 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 255 TYR 0.009 0.001 TYR B 245 PHE 0.009 0.001 PHE B 236 TRP 0.006 0.001 TRP E 224 HIS 0.004 0.001 HIS D 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (12965) covalent geometry : angle 0.49943 / 0.26 (17685) hydrogen bonds : bond 0.03592 / 2.34 ( 620) hydrogen bonds : angle 3.99333 / 2.76 ( 1995) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 150 time to evaluate : 0.456 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 151 average time/residue: 0.1081 time to fit residues: 24.5373 Evaluate side-chains 150 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 146 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 195 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 95 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.144507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.127992 restraints weight = 26925.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.129232 restraints weight = 26114.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.130096 restraints weight = 18370.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.131191 restraints weight = 14515.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.133504 restraints weight = 10956.014| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3362 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 12965 Z= 0.310 Angle : 0.694 7.637 17685 Z= 0.363 Chirality : 0.053 0.172 1960 Planarity : 0.005 0.032 2260 Dihedral : 4.901 18.702 1705 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.36 % Allowed : 11.70 % Favored : 87.94 % 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 (0.23), residues: 1545 helix: 1.97 (0.22), residues: 565 sheet: 0.80 (0.26), residues: 455 loop : -1.67 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 255 TYR 0.015 0.003 TYR C 135 PHE 0.021 0.002 PHE A 236 TRP 0.018 0.002 TRP E 224 HIS 0.008 0.002 HIS C 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00752 / 0.31 (12965) covalent geometry : angle 0.69408 / 0.36 (17685) hydrogen bonds : bond 0.05569 / 3.64 ( 620) hydrogen bonds : angle 4.44676 / 3.07 ( 1995) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 150 time to evaluate : 0.450 Fit side-chains REVERT: B 118 LEU cc_start: 0.8023 (mp) cc_final: 0.7719 (mt) REVERT: D 118 LEU cc_start: 0.8014 (mp) cc_final: 0.7665 (mt) outliers start: 5 outliers final: 3 residues processed: 151 average time/residue: 0.1062 time to fit residues: 24.4023 Evaluate side-chains 146 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 143 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 195 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 54 optimal weight: 0.0770 chunk 97 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 148 optimal weight: 0.0470 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.154801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.136013 restraints weight = 34034.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.138836 restraints weight = 25732.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.140509 restraints weight = 15080.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.142808 restraints weight = 10838.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.143047 restraints weight = 8556.399| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12965 Z= 0.101 Angle : 0.511 7.565 17685 Z= 0.263 Chirality : 0.045 0.144 1960 Planarity : 0.003 0.031 2260 Dihedral : 4.155 14.588 1705 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.14 % Allowed : 12.42 % Favored : 87.44 % 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: 1.03 (0.23), residues: 1545 helix: 2.39 (0.22), residues: 565 sheet: 0.91 (0.26), residues: 455 loop : -1.53 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 91 TYR 0.009 0.001 TYR E 245 PHE 0.007 0.001 PHE D 95 TRP 0.008 0.001 TRP E 43 HIS 0.004 0.001 HIS C 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (12965) covalent geometry : angle 0.51133 / 0.26 (17685) hydrogen bonds : bond 0.03461 / 2.28 ( 620) hydrogen bonds : angle 3.98751 / 2.75 ( 1995) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 142 time to evaluate : 0.510 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 143 average time/residue: 0.1064 time to fit residues: 22.8299 Evaluate side-chains 140 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain D residue 195 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 128 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 32 optimal weight: 7.9990 chunk 131 optimal weight: 0.6980 chunk 115 optimal weight: 6.9990 chunk 89 optimal weight: 0.2980 chunk 60 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.153890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.135156 restraints weight = 37394.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.137014 restraints weight = 29464.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.138536 restraints weight = 18455.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.140781 restraints weight = 12867.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.143233 restraints weight = 9038.078| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 12965 Z= 0.112 Angle : 0.507 7.577 17685 Z= 0.261 Chirality : 0.045 0.143 1960 Planarity : 0.003 0.033 2260 Dihedral : 4.116 14.538 1705 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.22 % Allowed : 12.27 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.23), residues: 1545 helix: 2.42 (0.22), residues: 565 sheet: 0.98 (0.26), residues: 455 loop : -1.53 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 255 TYR 0.011 0.001 TYR E 245 PHE 0.009 0.001 PHE D 95 TRP 0.006 0.001 TRP B 43 HIS 0.005 0.001 HIS C 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (12965) covalent geometry : angle 0.50698 / 0.26 (17685) hydrogen bonds : bond 0.03491 / 2.28 ( 620) hydrogen bonds : angle 3.95780 / 2.73 ( 1995) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 151 time to evaluate : 0.441 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 152 average time/residue: 0.1095 time to fit residues: 25.0715 Evaluate side-chains 147 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain D residue 195 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 108 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 37 optimal weight: 0.1980 chunk 88 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 95 optimal weight: 0.0970 chunk 71 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.157201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.137973 restraints weight = 46469.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.140798 restraints weight = 35895.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.142171 restraints weight = 17749.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.142994 restraints weight = 12348.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.142994 restraints weight = 10114.013| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 12965 Z= 0.093 Angle : 0.489 7.599 17685 Z= 0.250 Chirality : 0.045 0.139 1960 Planarity : 0.003 0.033 2260 Dihedral : 3.931 13.990 1705 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.29 % Allowed : 12.20 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.23), residues: 1545 helix: 2.45 (0.22), residues: 565 sheet: 1.09 (0.27), residues: 455 loop : -1.48 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 99 TYR 0.011 0.001 TYR E 245 PHE 0.008 0.001 PHE D 95 TRP 0.008 0.001 TRP E 161 HIS 0.004 0.001 HIS C 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 (12965) covalent geometry : angle 0.48889 / 0.25 (17685) hydrogen bonds : bond 0.03130 / 2.04 ( 620) hydrogen bonds : angle 3.87113 / 2.67 ( 1995) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1910.40 seconds wall clock time: 33 minutes 46.51 seconds (2026.51 seconds total)