Starting phenix.real_space_refine on Thu Sep 18 01:14:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ngg_49384/09_2025/9ngg_49384_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ngg_49384/09_2025/9ngg_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ngg_49384/09_2025/9ngg_49384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ngg_49384/09_2025/9ngg_49384.map" model { file = "/net/cci-nas-00/data/ceres_data/9ngg_49384/09_2025/9ngg_49384_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ngg_49384/09_2025/9ngg_49384_neut.cif" } 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-2.0-5805/lib/python3.9/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, 5 Unusual residues: {' NA': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 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: 5.26, per 1000 atoms: 0.42 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: 1.00 Conformation dependent library (CDL) restraints added in 987.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.51 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: 1.87 Time building geometry restraints manager: 1.36 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: 1.130 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 15.460 Find NCS groups from input model: 0.210 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 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 aren 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 covalent geometry : bond 0.00296 (12965) covalent geometry : angle 0.64076 (17685) hydrogen bonds : bond 0.18437 ( 620) hydrogen bonds : angle 6.82272 ( 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 : 0.374 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: 0.0877 time to fit residues: 23.5349 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 : 0.456 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 284 HIS B 284 HIS C 124 GLN C 284 HIS D 124 GLN D 284 HIS E 124 GLN E 151 ASN E 284 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.161886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.142744 restraints weight = 33372.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.144524 restraints weight = 21260.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.147771 restraints weight = 15556.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.148919 restraints weight = 9675.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.151008 restraints weight = 7598.796| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12965 Z= 0.114 Angle : 0.519 5.957 17685 Z= 0.274 Chirality : 0.046 0.155 1960 Planarity : 0.004 0.031 2260 Dihedral : 4.087 14.865 1705 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.02 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 aren not related in a simple way. whole: 0.84 (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 0.003 0.000 ARG D 99 TYR 0.008 0.001 TYR B 245 PHE 0.012 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 covalent geometry : bond 0.00249 (12965) covalent geometry : angle 0.51885 (17685) hydrogen bonds : bond 0.03983 ( 620) hydrogen bonds : angle 4.62503 ( 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 142 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.435 Fit side-chains REVERT: B 205 LEU cc_start: 0.8569 (tp) cc_final: 0.8346 (tp) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.0917 time to fit residues: 20.7310 Evaluate side-chains 128 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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: 0.3980 chunk 63 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 84 optimal weight: 0.2980 chunk 19 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 119 optimal weight: 0.3980 chunk 8 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.160787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.140362 restraints weight = 40409.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.144376 restraints weight = 27959.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.146027 restraints weight = 14290.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.149542 restraints weight = 9540.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.150127 restraints weight = 6650.261| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3569 r_free = 0.3569 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3569 r_free = 0.3569 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1451 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= 0.109 Angle : 0.496 5.861 17685 Z= 0.259 Chirality : 0.045 0.147 1960 Planarity : 0.004 0.026 2260 Dihedral : 3.927 14.787 1705 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.07 % Allowed : 8.81 % Favored : 91.12 % 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 aren not related in a simple way. whole: 1.05 (0.22), residues: 1545 helix: 2.15 (0.22), residues: 560 sheet: 1.35 (0.25), residues: 490 loop : -1.83 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 99 TYR 0.008 0.001 TYR B 245 PHE 0.009 0.001 PHE C 304 TRP 0.008 0.001 TRP A 43 HIS 0.005 0.001 HIS C 285 Details of bonding type rmsd covalent geometry : bond 0.00242 (12965) covalent geometry : angle 0.49557 (17685) hydrogen bonds : bond 0.03624 ( 620) hydrogen bonds : angle 4.16167 ( 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 135 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.467 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.0919 time to fit residues: 19.6669 Evaluate side-chains 128 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 136 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.143854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.124780 restraints weight = 35984.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.128815 restraints weight = 20960.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.130127 restraints weight = 13857.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.131974 restraints weight = 10868.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.132583 restraints weight = 9400.731| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 12965 Z= 0.342 Angle : 0.723 7.877 17685 Z= 0.382 Chirality : 0.054 0.179 1960 Planarity : 0.005 0.037 2260 Dihedral : 5.039 20.668 1705 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.87 % Allowed : 9.75 % Favored : 89.39 % 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 aren not related in a simple way. whole: 0.62 (0.22), residues: 1545 helix: 1.91 (0.22), residues: 560 sheet: 0.90 (0.26), residues: 455 loop : -1.76 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 255 TYR 0.015 0.003 TYR C 135 PHE 0.024 0.003 PHE A 236 TRP 0.019 0.003 TRP E 224 HIS 0.008 0.002 HIS D 285 Details of bonding type rmsd covalent geometry : bond 0.00836 (12965) covalent geometry : angle 0.72289 (17685) hydrogen bonds : bond 0.06005 ( 620) hydrogen bonds : angle 4.64869 ( 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 174 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 0.463 Fit side-chains REVERT: B 118 LEU cc_start: 0.8051 (mp) cc_final: 0.7728 (mt) REVERT: D 118 LEU cc_start: 0.8045 (mp) cc_final: 0.7696 (mt) outliers start: 12 outliers final: 9 residues processed: 168 average time/residue: 0.1060 time to fit residues: 26.7512 Evaluate side-chains 164 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 155 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain E residue 28 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 122 optimal weight: 0.9980 chunk 123 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 134 optimal weight: 0.0050 chunk 82 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.153731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.134832 restraints weight = 35820.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.137074 restraints weight = 28728.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.139028 restraints weight = 17689.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.142839 restraints weight = 11210.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.143104 restraints weight = 7849.455| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12965 Z= 0.112 Angle : 0.521 6.932 17685 Z= 0.270 Chirality : 0.046 0.144 1960 Planarity : 0.003 0.032 2260 Dihedral : 4.232 15.469 1705 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.14 % Allowed : 12.20 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.23), residues: 1545 helix: 2.30 (0.22), residues: 560 sheet: 0.92 (0.26), residues: 455 loop : -1.63 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 123 TYR 0.014 0.001 TYR B 270 PHE 0.008 0.001 PHE D 95 TRP 0.009 0.001 TRP B 43 HIS 0.004 0.001 HIS D 285 Details of bonding type rmsd covalent geometry : bond 0.00244 (12965) covalent geometry : angle 0.52132 (17685) hydrogen bonds : bond 0.03722 ( 620) hydrogen bonds : angle 4.09283 ( 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 151 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 149 time to evaluate : 0.484 Fit side-chains REVERT: D 34 LYS cc_start: 0.8663 (mttt) cc_final: 0.8458 (mttp) outliers start: 2 outliers final: 1 residues processed: 150 average time/residue: 0.1248 time to fit residues: 27.0017 Evaluate side-chains 141 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 28 THR 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: 8.9990 chunk 96 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.149322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.131679 restraints weight = 48075.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.132665 restraints weight = 47017.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.133991 restraints weight = 19374.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.135615 restraints weight = 12578.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.135681 restraints weight = 9615.523| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3443 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3443 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12965 Z= 0.173 Angle : 0.556 6.989 17685 Z= 0.289 Chirality : 0.047 0.150 1960 Planarity : 0.004 0.033 2260 Dihedral : 4.414 16.341 1705 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.29 % Allowed : 13.14 % Favored : 86.57 % 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 aren not related in a simple way. whole: 0.88 (0.23), residues: 1545 helix: 2.27 (0.22), residues: 560 sheet: 0.88 (0.26), residues: 455 loop : -1.63 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 255 TYR 0.012 0.002 TYR A 38 PHE 0.012 0.001 PHE A 236 TRP 0.009 0.001 TRP E 224 HIS 0.005 0.001 HIS D 285 Details of bonding type rmsd covalent geometry : bond 0.00414 (12965) covalent geometry : angle 0.55632 (17685) hydrogen bonds : bond 0.04257 ( 620) hydrogen bonds : angle 4.17674 ( 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 150 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 146 time to evaluate : 0.484 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 146 average time/residue: 0.1196 time to fit residues: 25.8752 Evaluate side-chains 146 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 144 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain D residue 28 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 113 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 13 optimal weight: 0.0000 chunk 73 optimal weight: 0.0270 chunk 149 optimal weight: 0.0070 chunk 15 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 overall best weight: 0.3460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.156729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.138319 restraints weight = 34108.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.141010 restraints weight = 26588.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.142713 restraints weight = 15602.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.145786 restraints weight = 10205.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.145851 restraints weight = 7495.195| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3572 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3572 r_free = 0.3572 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3572 r_free = 0.3572 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3572 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12965 Z= 0.092 Angle : 0.490 7.047 17685 Z= 0.252 Chirality : 0.045 0.139 1960 Planarity : 0.003 0.031 2260 Dihedral : 3.957 14.340 1705 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.14 % Allowed : 14.01 % Favored : 85.85 % 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 aren not related in a simple way. whole: 1.01 (0.23), residues: 1545 helix: 2.41 (0.22), residues: 560 sheet: 0.87 (0.26), residues: 470 loop : -1.58 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 99 TYR 0.011 0.001 TYR A 38 PHE 0.007 0.001 PHE D 95 TRP 0.008 0.001 TRP B 43 HIS 0.004 0.001 HIS C 285 Details of bonding type rmsd covalent geometry : bond 0.00195 (12965) covalent geometry : angle 0.48952 (17685) hydrogen bonds : bond 0.03180 ( 620) hydrogen bonds : angle 3.93975 ( 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 163 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 161 time to evaluate : 0.518 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 162 average time/residue: 0.1120 time to fit residues: 26.9601 Evaluate side-chains 154 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 70 optimal weight: 0.0170 chunk 127 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 131 optimal weight: 0.8980 overall best weight: 2.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.149511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.131332 restraints weight = 34555.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.132459 restraints weight = 26198.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.135170 restraints weight = 18949.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.136903 restraints weight = 11455.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.138100 restraints weight = 8955.095| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3486 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3486 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12965 Z= 0.179 Angle : 0.560 7.155 17685 Z= 0.290 Chirality : 0.047 0.150 1960 Planarity : 0.004 0.036 2260 Dihedral : 4.369 15.668 1705 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.22 % Allowed : 13.43 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.23), residues: 1545 helix: 2.37 (0.23), residues: 560 sheet: 0.91 (0.26), residues: 455 loop : -1.59 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 91 TYR 0.012 0.002 TYR A 38 PHE 0.012 0.001 PHE C 208 TRP 0.011 0.001 TRP C 224 HIS 0.006 0.001 HIS C 285 Details of bonding type rmsd covalent geometry : bond 0.00429 (12965) covalent geometry : angle 0.55957 (17685) hydrogen bonds : bond 0.04244 ( 620) hydrogen bonds : angle 4.12737 ( 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 149 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 146 time to evaluate : 0.427 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 146 average time/residue: 0.1170 time to fit residues: 24.9089 Evaluate side-chains 145 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 42 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 71 optimal weight: 0.0770 chunk 132 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 97 optimal weight: 0.0980 chunk 18 optimal weight: 0.8980 chunk 148 optimal weight: 0.0980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.157116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.138846 restraints weight = 34254.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.141068 restraints weight = 27238.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.142696 restraints weight = 18093.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.146657 restraints weight = 11372.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.146827 restraints weight = 7621.150| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- 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 = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12965 Z= 0.092 Angle : 0.491 7.238 17685 Z= 0.251 Chirality : 0.044 0.139 1960 Planarity : 0.003 0.032 2260 Dihedral : 3.932 13.969 1705 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.14 % Allowed : 13.65 % Favored : 86.21 % 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 aren not related in a simple way. whole: 1.12 (0.23), residues: 1545 helix: 2.47 (0.22), residues: 560 sheet: 1.05 (0.26), residues: 455 loop : -1.55 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 91 TYR 0.011 0.001 TYR A 38 PHE 0.007 0.001 PHE C 208 TRP 0.008 0.001 TRP B 43 HIS 0.004 0.001 HIS C 285 Details of bonding type rmsd covalent geometry : bond 0.00195 (12965) covalent geometry : angle 0.49059 (17685) hydrogen bonds : bond 0.03133 ( 620) hydrogen bonds : angle 3.89357 ( 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 148 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 146 time to evaluate : 0.474 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 147 average time/residue: 0.1161 time to fit residues: 24.6329 Evaluate side-chains 140 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 2 optimal weight: 8.9990 chunk 146 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 131 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.150806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.132105 restraints weight = 37631.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.133956 restraints weight = 28834.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.135920 restraints weight = 18717.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.139535 restraints weight = 11753.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.139596 restraints weight = 8365.511| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12965 Z= 0.156 Angle : 0.542 7.471 17685 Z= 0.280 Chirality : 0.046 0.147 1960 Planarity : 0.004 0.033 2260 Dihedral : 4.247 14.861 1705 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.07 % Allowed : 13.79 % Favored : 86.14 % 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 aren not related in a simple way. whole: 1.08 (0.23), residues: 1545 helix: 2.45 (0.22), residues: 560 sheet: 0.98 (0.26), residues: 455 loop : -1.54 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 91 TYR 0.012 0.002 TYR A 38 PHE 0.011 0.001 PHE B 236 TRP 0.010 0.001 TRP C 224 HIS 0.005 0.001 HIS D 285 Details of bonding type rmsd covalent geometry : bond 0.00373 (12965) covalent geometry : angle 0.54232 (17685) hydrogen bonds : bond 0.03957 ( 620) hydrogen bonds : angle 4.05755 ( 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 151 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.500 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 151 average time/residue: 0.1232 time to fit residues: 26.9214 Evaluate side-chains 148 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 37 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.150294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.131167 restraints weight = 46372.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.134258 restraints weight = 29673.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.135623 restraints weight = 15012.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.135623 restraints weight = 10759.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.135623 restraints weight = 10759.518| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3435 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12965 Z= 0.157 Angle : 0.547 7.571 17685 Z= 0.281 Chirality : 0.047 0.149 1960 Planarity : 0.004 0.033 2260 Dihedral : 4.329 15.379 1705 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.07 % Allowed : 13.86 % Favored : 86.06 % 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 aren not related in a simple way. whole: 1.00 (0.23), residues: 1545 helix: 2.39 (0.22), residues: 560 sheet: 0.95 (0.26), residues: 455 loop : -1.58 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 91 TYR 0.012 0.002 TYR A 38 PHE 0.011 0.001 PHE B 236 TRP 0.007 0.001 TRP C 224 HIS 0.006 0.001 HIS D 285 Details of bonding type rmsd covalent geometry : bond 0.00373 (12965) covalent geometry : angle 0.54692 (17685) hydrogen bonds : bond 0.04035 ( 620) hydrogen bonds : angle 4.07793 ( 1995) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1943.77 seconds wall clock time: 34 minutes 18.37 seconds (2058.37 seconds total)