Starting phenix.real_space_refine on Sat Aug 23 23:36:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gts_34266/08_2025/8gts_34266_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gts_34266/08_2025/8gts_34266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gts_34266/08_2025/8gts_34266_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gts_34266/08_2025/8gts_34266_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gts_34266/08_2025/8gts_34266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gts_34266/08_2025/8gts_34266.map" } resolution = 3.87 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= 0.001 sd= 0.030 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: 4 Type Number sf(0) Gaussians S 77 5.16 5 C 10290 2.51 5 N 2429 2.21 5 O 2674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15470 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2210 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 11, 'TRANS': 276} Chain breaks: 4 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'TYR:plan': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 61 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 1.70, per 1000 atoms: 0.11 Number of scatterers: 15470 At special positions: 0 Unit cell: (105.93, 108.07, 116.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 77 16.00 O 2674 8.00 N 2429 7.00 C 10290 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 663.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3934 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 7 sheets defined 69.8% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 removed outlier: 3.691A pdb=" N THR A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU A 9 " --> pdb=" O GLN A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 54 removed outlier: 3.633A pdb=" N LEU A 45 " --> pdb=" O ILE A 41 " (cutoff:3.500A) Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 73 through 87 Processing helix chain 'A' and resid 99 through 131 removed outlier: 4.420A pdb=" N LEU A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Proline residue: A 110 - end of helix Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 155 removed outlier: 4.089A pdb=" N ILE A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 removed outlier: 3.554A pdb=" N TYR A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 236 removed outlier: 3.649A pdb=" N THR A 220 " --> pdb=" O CYS A 216 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU A 221 " --> pdb=" O HIS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.975A pdb=" N LEU A 253 " --> pdb=" O SER A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 296 Proline residue: A 289 - end of helix removed outlier: 3.622A pdb=" N VAL A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 338 removed outlier: 3.739A pdb=" N TYR A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 355 removed outlier: 4.501A pdb=" N LYS A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 11 removed outlier: 3.691A pdb=" N THR B 8 " --> pdb=" O ALA B 4 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU B 9 " --> pdb=" O GLN B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 54 removed outlier: 3.633A pdb=" N LEU B 45 " --> pdb=" O ILE B 41 " (cutoff:3.500A) Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 73 through 87 Processing helix chain 'B' and resid 99 through 131 removed outlier: 4.420A pdb=" N LEU B 103 " --> pdb=" O GLY B 99 " (cutoff:3.500A) Proline residue: B 110 - end of helix Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 155 removed outlier: 4.089A pdb=" N ILE B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 removed outlier: 3.554A pdb=" N TYR B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 236 removed outlier: 3.649A pdb=" N THR B 220 " --> pdb=" O CYS B 216 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU B 221 " --> pdb=" O HIS B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 removed outlier: 3.975A pdb=" N LEU B 253 " --> pdb=" O SER B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 296 Proline residue: B 289 - end of helix removed outlier: 3.622A pdb=" N VAL B 292 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 338 removed outlier: 3.739A pdb=" N TYR B 331 " --> pdb=" O ASP B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 355 removed outlier: 4.501A pdb=" N LYS B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS B 347 " --> pdb=" O LYS B 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 11 removed outlier: 3.691A pdb=" N THR C 8 " --> pdb=" O ALA C 4 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU C 9 " --> pdb=" O GLN C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 54 removed outlier: 3.633A pdb=" N LEU C 45 " --> pdb=" O ILE C 41 " (cutoff:3.500A) Proline residue: C 46 - end of helix Processing helix chain 'C' and resid 73 through 87 Processing helix chain 'C' and resid 99 through 131 removed outlier: 4.419A pdb=" N LEU C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) Proline residue: C 110 - end of helix Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 155 removed outlier: 4.089A pdb=" N ILE C 135 " --> pdb=" O ALA C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 removed outlier: 3.554A pdb=" N TYR C 199 " --> pdb=" O ILE C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 236 removed outlier: 3.648A pdb=" N THR C 220 " --> pdb=" O CYS C 216 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU C 221 " --> pdb=" O HIS C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.975A pdb=" N LEU C 253 " --> pdb=" O SER C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 296 Proline residue: C 289 - end of helix removed outlier: 3.622A pdb=" N VAL C 292 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 338 removed outlier: 3.739A pdb=" N TYR C 331 " --> pdb=" O ASP C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 355 removed outlier: 4.501A pdb=" N LYS C 346 " --> pdb=" O VAL C 342 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS C 347 " --> pdb=" O LYS C 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 11 removed outlier: 3.690A pdb=" N THR D 8 " --> pdb=" O ALA D 4 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU D 9 " --> pdb=" O GLN D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 54 removed outlier: 3.633A pdb=" N LEU D 45 " --> pdb=" O ILE D 41 " (cutoff:3.500A) Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 73 through 87 Processing helix chain 'D' and resid 99 through 131 removed outlier: 4.420A pdb=" N LEU D 103 " --> pdb=" O GLY D 99 " (cutoff:3.500A) Proline residue: D 110 - end of helix Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 155 removed outlier: 4.089A pdb=" N ILE D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.554A pdb=" N TYR D 199 " --> pdb=" O ILE D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 236 removed outlier: 3.649A pdb=" N THR D 220 " --> pdb=" O CYS D 216 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU D 221 " --> pdb=" O HIS D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 255 removed outlier: 3.975A pdb=" N LEU D 253 " --> pdb=" O SER D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 296 Proline residue: D 289 - end of helix removed outlier: 3.623A pdb=" N VAL D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE D 296 " --> pdb=" O VAL D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 338 removed outlier: 3.739A pdb=" N TYR D 331 " --> pdb=" O ASP D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 355 removed outlier: 4.501A pdb=" N LYS D 346 " --> pdb=" O VAL D 342 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS D 347 " --> pdb=" O LYS D 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 11 removed outlier: 3.690A pdb=" N THR E 8 " --> pdb=" O ALA E 4 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU E 9 " --> pdb=" O GLN E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 54 removed outlier: 3.633A pdb=" N LEU E 45 " --> pdb=" O ILE E 41 " (cutoff:3.500A) Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 73 through 87 Processing helix chain 'E' and resid 99 through 131 removed outlier: 4.420A pdb=" N LEU E 103 " --> pdb=" O GLY E 99 " (cutoff:3.500A) Proline residue: E 110 - end of helix Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 155 removed outlier: 4.089A pdb=" N ILE E 135 " --> pdb=" O ALA E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.555A pdb=" N TYR E 199 " --> pdb=" O ILE E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 236 removed outlier: 3.649A pdb=" N THR E 220 " --> pdb=" O CYS E 216 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU E 221 " --> pdb=" O HIS E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 255 removed outlier: 3.976A pdb=" N LEU E 253 " --> pdb=" O SER E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 296 Proline residue: E 289 - end of helix removed outlier: 3.623A pdb=" N VAL E 292 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 338 removed outlier: 3.738A pdb=" N TYR E 331 " --> pdb=" O ASP E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 355 removed outlier: 4.502A pdb=" N LYS E 346 " --> pdb=" O VAL E 342 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS E 347 " --> pdb=" O LYS E 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 11 removed outlier: 3.691A pdb=" N THR F 8 " --> pdb=" O ALA F 4 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU F 9 " --> pdb=" O GLN F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 54 removed outlier: 3.633A pdb=" N LEU F 45 " --> pdb=" O ILE F 41 " (cutoff:3.500A) Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 73 through 87 Processing helix chain 'F' and resid 99 through 131 removed outlier: 4.419A pdb=" N LEU F 103 " --> pdb=" O GLY F 99 " (cutoff:3.500A) Proline residue: F 110 - end of helix Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 155 removed outlier: 4.089A pdb=" N ILE F 135 " --> pdb=" O ALA F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 206 removed outlier: 3.554A pdb=" N TYR F 199 " --> pdb=" O ILE F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 236 removed outlier: 3.649A pdb=" N THR F 220 " --> pdb=" O CYS F 216 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU F 221 " --> pdb=" O HIS F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 255 removed outlier: 3.975A pdb=" N LEU F 253 " --> pdb=" O SER F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 296 Proline residue: F 289 - end of helix removed outlier: 3.622A pdb=" N VAL F 292 " --> pdb=" O ALA F 288 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE F 296 " --> pdb=" O VAL F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 338 removed outlier: 3.739A pdb=" N TYR F 331 " --> pdb=" O ASP F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 355 removed outlier: 4.501A pdb=" N LYS F 346 " --> pdb=" O VAL F 342 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS F 347 " --> pdb=" O LYS F 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 11 removed outlier: 3.691A pdb=" N THR G 8 " --> pdb=" O ALA G 4 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU G 9 " --> pdb=" O GLN G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 54 removed outlier: 3.633A pdb=" N LEU G 45 " --> pdb=" O ILE G 41 " (cutoff:3.500A) Proline residue: G 46 - end of helix Processing helix chain 'G' and resid 73 through 87 Processing helix chain 'G' and resid 99 through 131 removed outlier: 4.421A pdb=" N LEU G 103 " --> pdb=" O GLY G 99 " (cutoff:3.500A) Proline residue: G 110 - end of helix Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 155 removed outlier: 4.089A pdb=" N ILE G 135 " --> pdb=" O ALA G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 removed outlier: 3.554A pdb=" N TYR G 199 " --> pdb=" O ILE G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 236 removed outlier: 3.650A pdb=" N THR G 220 " --> pdb=" O CYS G 216 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU G 221 " --> pdb=" O HIS G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 255 removed outlier: 3.975A pdb=" N LEU G 253 " --> pdb=" O SER G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 296 Proline residue: G 289 - end of helix removed outlier: 3.623A pdb=" N VAL G 292 " --> pdb=" O ALA G 288 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE G 296 " --> pdb=" O VAL G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 338 removed outlier: 3.739A pdb=" N TYR G 331 " --> pdb=" O ASP G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 355 removed outlier: 4.501A pdb=" N LYS G 346 " --> pdb=" O VAL G 342 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS G 347 " --> pdb=" O LYS G 343 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 removed outlier: 3.770A pdb=" N SER A 65 " --> pdb=" O LYS A 266 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS A 266 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 66 removed outlier: 3.771A pdb=" N SER B 65 " --> pdb=" O LYS B 266 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS B 266 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66 removed outlier: 3.769A pdb=" N SER C 65 " --> pdb=" O LYS C 266 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS C 266 " --> pdb=" O SER C 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 66 removed outlier: 3.769A pdb=" N SER D 65 " --> pdb=" O LYS D 266 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS D 266 " --> pdb=" O SER D 65 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 66 removed outlier: 3.770A pdb=" N SER E 65 " --> pdb=" O LYS E 266 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS E 266 " --> pdb=" O SER E 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 66 removed outlier: 3.770A pdb=" N SER F 65 " --> pdb=" O LYS F 266 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS F 266 " --> pdb=" O SER F 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 66 removed outlier: 3.770A pdb=" N SER G 65 " --> pdb=" O LYS G 266 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS G 266 " --> pdb=" O SER G 65 " (cutoff:3.500A) 938 hydrogen bonds defined for protein. 2751 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 1.32 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: 4615 1.34 - 1.46: 3610 1.46 - 1.58: 7483 1.58 - 1.69: 0 1.69 - 1.81: 91 Bond restraints: 15799 Sorted by residual: bond pdb=" C LEU D 45 " pdb=" N PRO D 46 " ideal model delta sigma weight residual 1.335 1.354 -0.018 1.36e-02 5.41e+03 1.83e+00 bond pdb=" C LEU C 45 " pdb=" N PRO C 46 " ideal model delta sigma weight residual 1.335 1.354 -0.018 1.36e-02 5.41e+03 1.80e+00 bond pdb=" C LEU A 45 " pdb=" N PRO A 46 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.36e-02 5.41e+03 1.75e+00 bond pdb=" C LEU E 45 " pdb=" N PRO E 46 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.36e-02 5.41e+03 1.74e+00 bond pdb=" C LEU F 45 " pdb=" N PRO F 46 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.36e-02 5.41e+03 1.73e+00 ... (remaining 15794 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 20719 1.47 - 2.95: 585 2.95 - 4.42: 130 4.42 - 5.90: 77 5.90 - 7.37: 7 Bond angle restraints: 21518 Sorted by residual: angle pdb=" N ILE F 3 " pdb=" CA ILE F 3 " pdb=" C ILE F 3 " ideal model delta sigma weight residual 112.96 109.05 3.91 1.00e+00 1.00e+00 1.53e+01 angle pdb=" N LYS B 140 " pdb=" CA LYS B 140 " pdb=" CB LYS B 140 " ideal model delta sigma weight residual 110.12 114.73 -4.61 1.47e+00 4.63e-01 9.82e+00 angle pdb=" N LYS D 140 " pdb=" CA LYS D 140 " pdb=" CB LYS D 140 " ideal model delta sigma weight residual 110.12 114.72 -4.60 1.47e+00 4.63e-01 9.78e+00 angle pdb=" N LYS A 140 " pdb=" CA LYS A 140 " pdb=" CB LYS A 140 " ideal model delta sigma weight residual 110.12 114.69 -4.57 1.47e+00 4.63e-01 9.67e+00 angle pdb=" N LYS G 140 " pdb=" CA LYS G 140 " pdb=" CB LYS G 140 " ideal model delta sigma weight residual 110.12 114.69 -4.57 1.47e+00 4.63e-01 9.66e+00 ... (remaining 21513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 8349 15.98 - 31.96: 730 31.96 - 47.94: 252 47.94 - 63.92: 49 63.92 - 79.90: 7 Dihedral angle restraints: 9387 sinusoidal: 3381 harmonic: 6006 Sorted by residual: dihedral pdb=" CA GLU C 352 " pdb=" C GLU C 352 " pdb=" N ASN C 353 " pdb=" CA ASN C 353 " ideal model delta harmonic sigma weight residual 180.00 160.24 19.76 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA GLU G 352 " pdb=" C GLU G 352 " pdb=" N ASN G 353 " pdb=" CA ASN G 353 " ideal model delta harmonic sigma weight residual 180.00 160.27 19.73 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA GLU A 352 " pdb=" C GLU A 352 " pdb=" N ASN A 353 " pdb=" CA ASN A 353 " ideal model delta harmonic sigma weight residual 180.00 160.28 19.72 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 9384 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1773 0.034 - 0.067: 637 0.067 - 0.101: 184 0.101 - 0.135: 52 0.135 - 0.168: 7 Chirality restraints: 2653 Sorted by residual: chirality pdb=" CA GLU D 352 " pdb=" N GLU D 352 " pdb=" C GLU D 352 " pdb=" CB GLU D 352 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.07e-01 chirality pdb=" CA GLU B 352 " pdb=" N GLU B 352 " pdb=" C GLU B 352 " pdb=" CB GLU B 352 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA GLU A 352 " pdb=" N GLU A 352 " pdb=" C GLU A 352 " pdb=" CB GLU A 352 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.73e-01 ... (remaining 2650 not shown) Planarity restraints: 2590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 123 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO B 124 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 124 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 124 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 123 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO E 124 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO E 124 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 124 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 123 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO C 124 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 124 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 124 " -0.019 5.00e-02 4.00e+02 ... (remaining 2587 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4097 2.80 - 3.33: 15636 3.33 - 3.85: 24909 3.85 - 4.38: 26262 4.38 - 4.90: 45522 Nonbonded interactions: 116426 Sorted by model distance: nonbonded pdb=" OG SER G 73 " pdb=" OE1 GLN G 76 " model vdw 2.279 3.040 nonbonded pdb=" OG SER C 73 " pdb=" OE1 GLN C 76 " model vdw 2.280 3.040 nonbonded pdb=" OG SER D 73 " pdb=" OE1 GLN D 76 " model vdw 2.280 3.040 nonbonded pdb=" OG SER A 73 " pdb=" OE1 GLN A 76 " model vdw 2.280 3.040 nonbonded pdb=" OG SER E 73 " pdb=" OE1 GLN E 76 " model vdw 2.280 3.040 ... (remaining 116421 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.040 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.510 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 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 0.036 15806 Z= 0.139 Angle : 0.672 7.374 21532 Z= 0.352 Chirality : 0.039 0.168 2653 Planarity : 0.004 0.033 2590 Dihedral : 14.162 79.903 5432 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.42 % Allowed : 0.12 % Favored : 99.46 % 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: 0.49 (0.20), residues: 1946 helix: 1.30 (0.15), residues: 1351 sheet: None (None), residues: 0 loop : -2.03 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 152 TYR 0.019 0.001 TYR D 230 PHE 0.009 0.001 PHE F 116 TRP 0.008 0.001 TRP D 104 HIS 0.001 0.001 HIS F 106 Details of bonding type rmsd covalent geometry : bond 0.00272 (15799) covalent geometry : angle 0.67197 (21518) SS BOND : bond 0.00213 ( 7) SS BOND : angle 0.85728 ( 14) hydrogen bonds : bond 0.14877 ( 938) hydrogen bonds : angle 4.33482 ( 2751) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 259 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: A 261 ASP cc_start: 0.7862 (m-30) cc_final: 0.7542 (m-30) REVERT: B 261 ASP cc_start: 0.7780 (m-30) cc_final: 0.7575 (p0) REVERT: C 37 MET cc_start: 0.6277 (tpp) cc_final: 0.5980 (tpp) REVERT: C 75 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.7127 (tpp-160) REVERT: C 224 ILE cc_start: 0.7368 (mm) cc_final: 0.7157 (mt) REVERT: D 75 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.7140 (tpp-160) REVERT: D 198 GLN cc_start: 0.7449 (mp-120) cc_final: 0.7197 (mp-120) REVERT: E 75 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6872 (tpp-160) REVERT: E 261 ASP cc_start: 0.7667 (m-30) cc_final: 0.7366 (m-30) REVERT: F 75 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7113 (tpp-160) REVERT: F 224 ILE cc_start: 0.7200 (mm) cc_final: 0.6989 (mt) REVERT: F 261 ASP cc_start: 0.7898 (m-30) cc_final: 0.7524 (m-30) REVERT: F 296 PHE cc_start: 0.7527 (m-10) cc_final: 0.7236 (m-10) REVERT: G 75 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7197 (tpp-160) REVERT: G 261 ASP cc_start: 0.7668 (m-30) cc_final: 0.7424 (p0) outliers start: 7 outliers final: 0 residues processed: 259 average time/residue: 0.0973 time to fit residues: 38.8529 Evaluate side-chains 222 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 217 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain D residue 75 ARG Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain G residue 75 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4146 r_free = 0.4146 target = 0.182620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.135134 restraints weight = 20314.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.139914 restraints weight = 12056.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.143095 restraints weight = 8599.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.144989 restraints weight = 6903.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.146572 restraints weight = 6005.703| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15806 Z= 0.128 Angle : 0.612 6.301 21532 Z= 0.304 Chirality : 0.040 0.128 2653 Planarity : 0.004 0.030 2590 Dihedral : 5.489 59.990 2120 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.39 % Allowed : 11.26 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.20), residues: 1946 helix: 1.48 (0.15), residues: 1358 sheet: None (None), residues: 0 loop : -2.06 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 75 TYR 0.022 0.001 TYR D 121 PHE 0.011 0.001 PHE F 244 TRP 0.008 0.001 TRP C 104 HIS 0.003 0.001 HIS G 217 Details of bonding type rmsd covalent geometry : bond 0.00291 (15799) covalent geometry : angle 0.61127 (21518) SS BOND : bond 0.00422 ( 7) SS BOND : angle 1.53645 ( 14) hydrogen bonds : bond 0.03569 ( 938) hydrogen bonds : angle 3.49394 ( 2751) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 233 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ASP cc_start: 0.7981 (m-30) cc_final: 0.7640 (m-30) REVERT: A 334 PHE cc_start: 0.7145 (m-10) cc_final: 0.6799 (m-80) REVERT: B 234 TYR cc_start: 0.7944 (t80) cc_final: 0.7692 (t80) REVERT: B 261 ASP cc_start: 0.7916 (m-30) cc_final: 0.7569 (p0) REVERT: B 334 PHE cc_start: 0.7017 (m-10) cc_final: 0.6608 (m-80) REVERT: C 37 MET cc_start: 0.6276 (tpp) cc_final: 0.5875 (tpp) REVERT: C 75 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.7013 (tpp-160) REVERT: C 224 ILE cc_start: 0.7259 (mm) cc_final: 0.6990 (mt) REVERT: C 334 PHE cc_start: 0.7039 (m-10) cc_final: 0.6614 (m-80) REVERT: D 75 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.7022 (tpp-160) REVERT: D 147 ASP cc_start: 0.8033 (t70) cc_final: 0.7680 (t0) REVERT: D 334 PHE cc_start: 0.6873 (m-10) cc_final: 0.6478 (m-80) REVERT: E 75 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6845 (tpp-160) REVERT: E 334 PHE cc_start: 0.6855 (m-10) cc_final: 0.6483 (m-80) REVERT: F 75 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6941 (tpp-160) REVERT: F 224 ILE cc_start: 0.7121 (mm) cc_final: 0.6892 (mt) REVERT: F 261 ASP cc_start: 0.8026 (m-30) cc_final: 0.7650 (m-30) REVERT: F 334 PHE cc_start: 0.7145 (m-10) cc_final: 0.6885 (m-80) REVERT: G 75 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.7148 (tpp-160) REVERT: G 261 ASP cc_start: 0.7766 (m-30) cc_final: 0.7485 (p0) REVERT: G 334 PHE cc_start: 0.7038 (m-10) cc_final: 0.6830 (m-80) outliers start: 23 outliers final: 18 residues processed: 240 average time/residue: 0.1129 time to fit residues: 42.6677 Evaluate side-chains 236 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain D residue 75 ARG Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 347 CYS Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 347 CYS Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 75 ARG Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 347 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 185 optimal weight: 0.5980 chunk 71 optimal weight: 7.9990 chunk 179 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 148 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.4091 r_free = 0.4091 target = 0.176917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.128802 restraints weight = 20906.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.133543 restraints weight = 12502.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.136646 restraints weight = 8970.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.138682 restraints weight = 7217.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.139805 restraints weight = 6273.282| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15806 Z= 0.158 Angle : 0.641 9.169 21532 Z= 0.317 Chirality : 0.040 0.120 2653 Planarity : 0.004 0.038 2590 Dihedral : 5.410 59.442 2120 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.54 % Allowed : 15.01 % Favored : 82.45 % 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: 0.47 (0.20), residues: 1946 helix: 1.25 (0.15), residues: 1400 sheet: None (None), residues: 0 loop : -2.20 (0.24), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 75 TYR 0.025 0.002 TYR F 121 PHE 0.012 0.001 PHE C 244 TRP 0.006 0.001 TRP C 104 HIS 0.003 0.001 HIS E 134 Details of bonding type rmsd covalent geometry : bond 0.00379 (15799) covalent geometry : angle 0.64032 (21518) SS BOND : bond 0.00502 ( 7) SS BOND : angle 1.61883 ( 14) hydrogen bonds : bond 0.04061 ( 938) hydrogen bonds : angle 3.56067 ( 2751) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 231 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 334 PHE cc_start: 0.7215 (m-10) cc_final: 0.6878 (m-80) REVERT: B 334 PHE cc_start: 0.7149 (m-10) cc_final: 0.6723 (m-80) REVERT: C 37 MET cc_start: 0.6111 (tpp) cc_final: 0.5572 (tpp) REVERT: C 75 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6940 (tpp-160) REVERT: C 198 GLN cc_start: 0.7956 (mp-120) cc_final: 0.7436 (mp10) REVERT: C 256 ASP cc_start: 0.6878 (t0) cc_final: 0.6638 (t0) REVERT: C 334 PHE cc_start: 0.7194 (m-10) cc_final: 0.6734 (m-80) REVERT: D 198 GLN cc_start: 0.7307 (mp-120) cc_final: 0.6970 (mp10) REVERT: D 334 PHE cc_start: 0.7047 (m-10) cc_final: 0.6647 (m-80) REVERT: E 334 PHE cc_start: 0.7226 (m-10) cc_final: 0.6853 (m-80) REVERT: F 198 GLN cc_start: 0.7627 (mp-120) cc_final: 0.6949 (mp10) REVERT: F 334 PHE cc_start: 0.7401 (m-10) cc_final: 0.7168 (m-80) REVERT: G 75 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.7124 (tpp-160) REVERT: G 334 PHE cc_start: 0.7186 (m-10) cc_final: 0.6983 (m-80) outliers start: 42 outliers final: 24 residues processed: 250 average time/residue: 0.1170 time to fit residues: 45.2300 Evaluate side-chains 240 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 214 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 347 CYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain G residue 75 ARG Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 347 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 164 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 106 optimal weight: 0.4980 chunk 150 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 115 optimal weight: 0.7980 chunk 177 optimal weight: 0.9980 chunk 154 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4118 r_free = 0.4118 target = 0.179263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.131563 restraints weight = 20614.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.136432 restraints weight = 12289.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.139632 restraints weight = 8757.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.141778 restraints weight = 7003.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.143062 restraints weight = 6058.678| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15806 Z= 0.126 Angle : 0.630 11.984 21532 Z= 0.297 Chirality : 0.039 0.115 2653 Planarity : 0.004 0.038 2590 Dihedral : 4.368 59.853 2108 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.21 % Allowed : 17.74 % Favored : 79.06 % 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: 0.66 (0.20), residues: 1946 helix: 1.36 (0.15), residues: 1400 sheet: None (None), residues: 0 loop : -2.05 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 75 TYR 0.024 0.001 TYR D 121 PHE 0.011 0.001 PHE C 244 TRP 0.008 0.001 TRP G 104 HIS 0.002 0.001 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00291 (15799) covalent geometry : angle 0.62911 (21518) SS BOND : bond 0.00325 ( 7) SS BOND : angle 1.27161 ( 14) hydrogen bonds : bond 0.03410 ( 938) hydrogen bonds : angle 3.38008 ( 2751) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 244 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLN cc_start: 0.8485 (pm20) cc_final: 0.8129 (mt0) REVERT: A 334 PHE cc_start: 0.7168 (m-10) cc_final: 0.6883 (m-80) REVERT: B 334 PHE cc_start: 0.7170 (m-10) cc_final: 0.6721 (m-80) REVERT: C 37 MET cc_start: 0.6006 (tpp) cc_final: 0.5508 (tpp) REVERT: C 75 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.7090 (mmm160) REVERT: C 198 GLN cc_start: 0.7862 (mp-120) cc_final: 0.7105 (mp10) REVERT: C 334 PHE cc_start: 0.7093 (m-10) cc_final: 0.6673 (m-80) REVERT: D 334 PHE cc_start: 0.7036 (m-10) cc_final: 0.6673 (m-80) REVERT: F 37 MET cc_start: 0.4999 (tpp) cc_final: 0.4784 (tpp) REVERT: F 198 GLN cc_start: 0.7610 (mp-120) cc_final: 0.6998 (mp10) REVERT: G 75 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7049 (tpp-160) REVERT: G 334 PHE cc_start: 0.7008 (m-10) cc_final: 0.6755 (m-80) outliers start: 53 outliers final: 44 residues processed: 269 average time/residue: 0.1166 time to fit residues: 48.5470 Evaluate side-chains 273 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 227 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 347 CYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 294 THR Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 75 ARG Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 347 CYS Chi-restraints excluded: chain G residue 352 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 173 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 165 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 67 optimal weight: 0.0470 chunk 76 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.2882 ------------------------------------------------------------------------------- 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 = 0.4073 r_free = 0.4073 target = 0.174888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.126880 restraints weight = 20974.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.131558 restraints weight = 12740.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.134649 restraints weight = 9183.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.136694 restraints weight = 7420.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.137878 restraints weight = 6446.363| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15806 Z= 0.164 Angle : 0.672 10.065 21532 Z= 0.325 Chirality : 0.041 0.124 2653 Planarity : 0.004 0.040 2590 Dihedral : 4.532 58.389 2108 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.42 % Allowed : 19.85 % Favored : 77.72 % 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: 0.53 (0.20), residues: 1946 helix: 1.25 (0.15), residues: 1400 sheet: None (None), residues: 0 loop : -2.04 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 75 TYR 0.026 0.002 TYR F 121 PHE 0.014 0.001 PHE E 334 TRP 0.004 0.001 TRP B 74 HIS 0.003 0.001 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00397 (15799) covalent geometry : angle 0.67087 (21518) SS BOND : bond 0.00538 ( 7) SS BOND : angle 1.44224 ( 14) hydrogen bonds : bond 0.04025 ( 938) hydrogen bonds : angle 3.57625 ( 2751) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 232 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 PHE cc_start: 0.7321 (m-10) cc_final: 0.7029 (m-80) REVERT: B 334 PHE cc_start: 0.7189 (m-10) cc_final: 0.6792 (m-80) REVERT: C 37 MET cc_start: 0.5749 (tpp) cc_final: 0.5238 (tpp) REVERT: C 75 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7012 (tpp-160) REVERT: C 198 GLN cc_start: 0.7914 (mp-120) cc_final: 0.7169 (mp10) REVERT: C 256 ASP cc_start: 0.6963 (t0) cc_final: 0.6687 (t0) REVERT: C 262 GLN cc_start: 0.8425 (pm20) cc_final: 0.8082 (pm20) REVERT: C 334 PHE cc_start: 0.7156 (m-10) cc_final: 0.6777 (m-80) REVERT: D 334 PHE cc_start: 0.7204 (m-10) cc_final: 0.6884 (m-80) REVERT: F 37 MET cc_start: 0.4887 (tpp) cc_final: 0.4673 (tpp) REVERT: F 198 GLN cc_start: 0.7652 (mp-120) cc_final: 0.7084 (mp10) REVERT: G 75 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.7101 (tpp-160) REVERT: G 334 PHE cc_start: 0.7160 (m-10) cc_final: 0.6957 (m-80) outliers start: 40 outliers final: 37 residues processed: 250 average time/residue: 0.1138 time to fit residues: 44.5048 Evaluate side-chains 263 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 224 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 294 THR Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain G residue 75 ARG Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 347 CYS Chi-restraints excluded: chain G residue 352 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 55 optimal weight: 0.3980 chunk 135 optimal weight: 0.4980 chunk 69 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 105 optimal weight: 0.5980 chunk 178 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 192 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4126 r_free = 0.4126 target = 0.180010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.131879 restraints weight = 20772.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.136820 restraints weight = 12422.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.140118 restraints weight = 8858.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.142220 restraints weight = 7085.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.143468 restraints weight = 6130.383| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15806 Z= 0.114 Angle : 0.618 12.295 21532 Z= 0.291 Chirality : 0.039 0.113 2653 Planarity : 0.004 0.040 2590 Dihedral : 4.126 58.210 2108 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.91 % Allowed : 20.46 % Favored : 76.63 % 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 (0.20), residues: 1946 helix: 1.63 (0.15), residues: 1351 sheet: None (None), residues: 0 loop : -1.87 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 75 TYR 0.024 0.002 TYR F 121 PHE 0.011 0.001 PHE C 244 TRP 0.009 0.001 TRP G 104 HIS 0.003 0.001 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00252 (15799) covalent geometry : angle 0.61766 (21518) SS BOND : bond 0.00209 ( 7) SS BOND : angle 1.13688 ( 14) hydrogen bonds : bond 0.03123 ( 938) hydrogen bonds : angle 3.30255 ( 2751) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 243 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLN cc_start: 0.8585 (pm20) cc_final: 0.8188 (mt0) REVERT: B 334 PHE cc_start: 0.7088 (m-10) cc_final: 0.6701 (m-80) REVERT: B 352 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7662 (pp20) REVERT: C 37 MET cc_start: 0.5709 (tpp) cc_final: 0.5256 (tpp) REVERT: C 75 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.7078 (mmm160) REVERT: C 198 GLN cc_start: 0.7680 (mp-120) cc_final: 0.7007 (mp10) REVERT: C 334 PHE cc_start: 0.7054 (m-10) cc_final: 0.6681 (m-80) REVERT: D 334 PHE cc_start: 0.7078 (m-10) cc_final: 0.6771 (m-80) REVERT: E 262 GLN cc_start: 0.8397 (pm20) cc_final: 0.8166 (mt0) REVERT: F 198 GLN cc_start: 0.7531 (mp-120) cc_final: 0.7006 (mp10) REVERT: F 262 GLN cc_start: 0.8524 (pm20) cc_final: 0.8230 (mt0) REVERT: G 75 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.7050 (tpp-160) REVERT: G 334 PHE cc_start: 0.6929 (m-10) cc_final: 0.6662 (m-80) outliers start: 48 outliers final: 39 residues processed: 264 average time/residue: 0.1152 time to fit residues: 47.1389 Evaluate side-chains 274 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 232 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 352 GLU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 75 ARG Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 352 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 58 optimal weight: 0.8980 chunk 109 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 175 optimal weight: 0.0870 chunk 164 optimal weight: 3.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.4118 r_free = 0.4118 target = 0.179121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.131236 restraints weight = 20684.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.136050 restraints weight = 12294.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.139291 restraints weight = 8769.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.141435 restraints weight = 7015.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.142451 restraints weight = 6054.458| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15806 Z= 0.117 Angle : 0.627 12.920 21532 Z= 0.295 Chirality : 0.039 0.115 2653 Planarity : 0.004 0.040 2590 Dihedral : 4.067 57.974 2108 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.15 % Allowed : 21.85 % Favored : 75.00 % 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: 0.99 (0.20), residues: 1946 helix: 1.64 (0.15), residues: 1358 sheet: None (None), residues: 0 loop : -1.75 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 75 TYR 0.025 0.002 TYR A 121 PHE 0.011 0.001 PHE B 244 TRP 0.008 0.001 TRP C 104 HIS 0.003 0.001 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00263 (15799) covalent geometry : angle 0.62699 (21518) SS BOND : bond 0.00247 ( 7) SS BOND : angle 1.15304 ( 14) hydrogen bonds : bond 0.03149 ( 938) hydrogen bonds : angle 3.27663 ( 2751) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 229 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8144 (mt0) REVERT: B 334 PHE cc_start: 0.7074 (m-10) cc_final: 0.6706 (m-80) REVERT: C 37 MET cc_start: 0.5941 (tpp) cc_final: 0.5560 (tpp) REVERT: C 75 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7107 (tpp-160) REVERT: C 198 GLN cc_start: 0.7677 (mp-120) cc_final: 0.6982 (mp10) REVERT: C 256 ASP cc_start: 0.7055 (t0) cc_final: 0.6788 (t0) REVERT: C 334 PHE cc_start: 0.6932 (m-10) cc_final: 0.6559 (m-80) REVERT: D 334 PHE cc_start: 0.7074 (m-10) cc_final: 0.6770 (m-80) REVERT: F 37 MET cc_start: 0.4955 (tpp) cc_final: 0.4677 (tpp) REVERT: F 198 GLN cc_start: 0.7345 (mp-120) cc_final: 0.7077 (mp10) REVERT: F 262 GLN cc_start: 0.8450 (pm20) cc_final: 0.8198 (mt0) REVERT: G 334 PHE cc_start: 0.6917 (m-10) cc_final: 0.6643 (m-80) REVERT: G 352 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7684 (pp20) outliers start: 52 outliers final: 41 residues processed: 255 average time/residue: 0.1158 time to fit residues: 45.8227 Evaluate side-chains 267 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 223 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 352 GLU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 352 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 26 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 143 optimal weight: 0.0670 chunk 28 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 155 optimal weight: 0.8980 chunk 49 optimal weight: 0.3980 chunk 128 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 162 optimal weight: 0.6980 chunk 119 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 198 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.179942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.132190 restraints weight = 20809.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.137017 restraints weight = 12294.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.140263 restraints weight = 8750.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.142410 restraints weight = 7000.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.143786 restraints weight = 6036.369| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15806 Z= 0.114 Angle : 0.623 12.894 21532 Z= 0.293 Chirality : 0.039 0.115 2653 Planarity : 0.004 0.041 2590 Dihedral : 3.764 57.942 2104 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.91 % Allowed : 22.76 % Favored : 74.33 % 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 (0.20), residues: 1946 helix: 1.71 (0.15), residues: 1351 sheet: None (None), residues: 0 loop : -1.85 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 75 TYR 0.026 0.002 TYR F 121 PHE 0.011 0.001 PHE C 244 TRP 0.008 0.001 TRP G 104 HIS 0.002 0.001 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00256 (15799) covalent geometry : angle 0.62234 (21518) SS BOND : bond 0.00232 ( 7) SS BOND : angle 1.13870 ( 14) hydrogen bonds : bond 0.02990 ( 938) hydrogen bonds : angle 3.24094 ( 2751) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 234 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8184 (mt0) REVERT: B 334 PHE cc_start: 0.7110 (m-10) cc_final: 0.6745 (m-80) REVERT: B 352 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7631 (pp20) REVERT: C 37 MET cc_start: 0.5903 (tpp) cc_final: 0.5472 (tpp) REVERT: C 75 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.7032 (tpp-160) REVERT: C 198 GLN cc_start: 0.7649 (mp-120) cc_final: 0.6950 (mp10) REVERT: C 256 ASP cc_start: 0.7185 (t0) cc_final: 0.6887 (t0) REVERT: C 334 PHE cc_start: 0.6879 (m-10) cc_final: 0.6530 (m-80) REVERT: C 352 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7708 (pp20) REVERT: D 334 PHE cc_start: 0.7055 (m-10) cc_final: 0.6724 (m-80) REVERT: F 37 MET cc_start: 0.4916 (tpp) cc_final: 0.4667 (tpp) REVERT: F 262 GLN cc_start: 0.8400 (pm20) cc_final: 0.8174 (mt0) REVERT: G 334 PHE cc_start: 0.6942 (m-10) cc_final: 0.6667 (m-80) REVERT: G 352 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7686 (pp20) outliers start: 48 outliers final: 41 residues processed: 253 average time/residue: 0.1186 time to fit residues: 46.2258 Evaluate side-chains 271 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 225 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 352 GLU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 352 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 99 optimal weight: 0.9980 chunk 150 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 155 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 169 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 148 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 87 optimal weight: 0.0010 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 198 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.179175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.131216 restraints weight = 20759.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.136042 restraints weight = 12396.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.139227 restraints weight = 8830.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.141355 restraints weight = 7098.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.142530 restraints weight = 6127.664| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15806 Z= 0.119 Angle : 0.638 13.236 21532 Z= 0.300 Chirality : 0.039 0.117 2653 Planarity : 0.004 0.041 2590 Dihedral : 3.786 58.040 2104 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.97 % Allowed : 23.31 % Favored : 73.73 % 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 (0.20), residues: 1946 helix: 1.66 (0.15), residues: 1358 sheet: None (None), residues: 0 loop : -1.76 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 75 TYR 0.027 0.002 TYR F 121 PHE 0.011 0.001 PHE B 244 TRP 0.007 0.001 TRP C 104 HIS 0.003 0.001 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00271 (15799) covalent geometry : angle 0.63761 (21518) SS BOND : bond 0.00268 ( 7) SS BOND : angle 1.11413 ( 14) hydrogen bonds : bond 0.03072 ( 938) hydrogen bonds : angle 3.24763 ( 2751) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 227 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8224 (mt0) REVERT: A 352 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7494 (pp20) REVERT: B 334 PHE cc_start: 0.7137 (m-10) cc_final: 0.6754 (m-80) REVERT: B 352 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7613 (pp20) REVERT: C 37 MET cc_start: 0.6001 (tpp) cc_final: 0.5579 (tpp) REVERT: C 75 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.7044 (tpp-160) REVERT: C 198 GLN cc_start: 0.7620 (mp-120) cc_final: 0.6756 (mp10) REVERT: C 256 ASP cc_start: 0.7335 (t0) cc_final: 0.6981 (t0) REVERT: C 334 PHE cc_start: 0.6982 (m-10) cc_final: 0.6623 (m-80) REVERT: C 352 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7699 (pp20) REVERT: D 334 PHE cc_start: 0.7119 (m-10) cc_final: 0.6802 (m-80) REVERT: D 352 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7659 (pp20) REVERT: F 37 MET cc_start: 0.5007 (tpp) cc_final: 0.4770 (tpp) REVERT: F 352 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7698 (pp20) REVERT: G 334 PHE cc_start: 0.6943 (m-10) cc_final: 0.6663 (m-80) REVERT: G 352 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7649 (pp20) outliers start: 49 outliers final: 38 residues processed: 246 average time/residue: 0.1180 time to fit residues: 44.9229 Evaluate side-chains 270 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 224 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 352 GLU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 352 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 70 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 138 optimal weight: 0.0570 chunk 23 optimal weight: 0.8980 chunk 85 optimal weight: 20.0000 chunk 186 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 overall best weight: 0.6700 ------------------------------------------------------------------------------- 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 = 0.4121 r_free = 0.4121 target = 0.179387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.131348 restraints weight = 20841.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.136049 restraints weight = 12458.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.139226 restraints weight = 8939.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.141074 restraints weight = 7188.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.142639 restraints weight = 6255.163| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15806 Z= 0.120 Angle : 0.641 13.630 21532 Z= 0.302 Chirality : 0.039 0.115 2653 Planarity : 0.004 0.041 2590 Dihedral : 3.770 58.061 2104 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.78 % Allowed : 23.43 % Favored : 73.79 % 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 (0.20), residues: 1946 helix: 1.70 (0.15), residues: 1351 sheet: None (None), residues: 0 loop : -1.84 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 75 TYR 0.028 0.002 TYR F 121 PHE 0.011 0.001 PHE C 244 TRP 0.007 0.001 TRP C 104 HIS 0.002 0.001 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00274 (15799) covalent geometry : angle 0.64022 (21518) SS BOND : bond 0.00257 ( 7) SS BOND : angle 1.10588 ( 14) hydrogen bonds : bond 0.03064 ( 938) hydrogen bonds : angle 3.24671 ( 2751) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 226 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 PHE cc_start: 0.6991 (m-80) cc_final: 0.6730 (m-80) REVERT: B 334 PHE cc_start: 0.7128 (m-10) cc_final: 0.6747 (m-80) REVERT: B 352 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7247 (pp20) REVERT: C 37 MET cc_start: 0.5965 (tpp) cc_final: 0.5555 (tpp) REVERT: C 75 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.7033 (tpp-160) REVERT: C 198 GLN cc_start: 0.7619 (mp-120) cc_final: 0.6755 (mp10) REVERT: C 256 ASP cc_start: 0.7363 (t0) cc_final: 0.7001 (t0) REVERT: C 334 PHE cc_start: 0.6966 (m-10) cc_final: 0.6614 (m-80) REVERT: C 352 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7275 (pp20) REVERT: D 334 PHE cc_start: 0.7109 (m-10) cc_final: 0.6785 (m-80) REVERT: D 352 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7603 (pp20) REVERT: F 352 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7719 (pp20) REVERT: G 334 PHE cc_start: 0.7050 (m-10) cc_final: 0.6773 (m-80) REVERT: G 352 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7535 (pp20) outliers start: 46 outliers final: 36 residues processed: 244 average time/residue: 0.1129 time to fit residues: 43.0518 Evaluate side-chains 265 residues out of total 1834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 223 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 352 GLU Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 352 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 108 optimal weight: 0.0040 chunk 163 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 115 optimal weight: 0.0050 chunk 35 optimal weight: 0.0870 chunk 5 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.3984 ------------------------------------------------------------------------------- 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 = 0.4145 r_free = 0.4145 target = 0.181688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.133912 restraints weight = 20556.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.138818 restraints weight = 12157.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.142027 restraints weight = 8629.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.144175 restraints weight = 6904.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.145411 restraints weight = 5955.313| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15806 Z= 0.108 Angle : 0.631 13.354 21532 Z= 0.294 Chirality : 0.038 0.115 2653 Planarity : 0.004 0.043 2590 Dihedral : 3.618 58.001 2104 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.48 % Allowed : 23.61 % Favored : 73.91 % 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 (0.20), residues: 1946 helix: 1.79 (0.15), residues: 1351 sheet: None (None), residues: 0 loop : -1.82 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 75 TYR 0.027 0.002 TYR A 121 PHE 0.009 0.001 PHE B 244 TRP 0.009 0.001 TRP C 104 HIS 0.002 0.001 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00233 (15799) covalent geometry : angle 0.63091 (21518) SS BOND : bond 0.00150 ( 7) SS BOND : angle 1.02668 ( 14) hydrogen bonds : bond 0.02710 ( 938) hydrogen bonds : angle 3.15255 ( 2751) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2350.46 seconds wall clock time: 41 minutes 52.76 seconds (2512.76 seconds total)