Starting phenix.real_space_refine on Sun Aug 24 07:23:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bz8_45056/08_2025/9bz8_45056.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bz8_45056/08_2025/9bz8_45056.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bz8_45056/08_2025/9bz8_45056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bz8_45056/08_2025/9bz8_45056.map" model { file = "/net/cci-nas-00/data/ceres_data/9bz8_45056/08_2025/9bz8_45056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bz8_45056/08_2025/9bz8_45056.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 12215 2.51 5 N 2814 2.21 5 O 3171 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s 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: 18277 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2611 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 14, 'TRANS': 307} Chain breaks: 3 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 2.47, per 1000 atoms: 0.14 Number of scatterers: 18277 At special positions: 0 Unit cell: (113.42, 113.42, 121.98, 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 3171 8.00 N 2814 7.00 C 12215 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 267 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 267 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 267 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 267 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 267 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 267 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 267 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 248 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 248 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 248 " 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: 1.56 Conformation dependent library (CDL) restraints added in 683.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4382 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 7 sheets defined 72.4% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 32 through 54 Proline residue: A 46 - end of helix removed outlier: 3.690A pdb=" N PHE A 54 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 91 removed outlier: 4.443A pdb=" N GLN A 89 " --> pdb=" O TRP A 85 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN A 90 " --> pdb=" O ALA A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 131 Proline residue: A 110 - end of helix Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 158 Processing helix chain 'A' and resid 197 through 207 removed outlier: 3.795A pdb=" N ASN A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 240 Processing helix chain 'A' and resid 252 through 256 removed outlier: 4.280A pdb=" N LEU A 255 " --> pdb=" O THR A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 298 Proline residue: A 291 - end of helix removed outlier: 3.687A pdb=" N ILE A 294 " --> pdb=" O MET A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.919A pdb=" N TYR A 311 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 340 Processing helix chain 'A' and resid 341 through 344 Processing helix chain 'A' and resid 345 through 360 removed outlier: 3.774A pdb=" N THR A 359 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY A 360 " --> pdb=" O ILE A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 372 removed outlier: 4.201A pdb=" N TYR A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 11 Processing helix chain 'B' and resid 32 through 54 Proline residue: B 46 - end of helix removed outlier: 3.691A pdb=" N PHE B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 91 removed outlier: 4.442A pdb=" N GLN B 89 " --> pdb=" O TRP B 85 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN B 90 " --> pdb=" O ALA B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 131 Proline residue: B 110 - end of helix Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 158 Processing helix chain 'B' and resid 197 through 207 removed outlier: 3.794A pdb=" N ASN B 207 " --> pdb=" O LYS B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 240 Processing helix chain 'B' and resid 252 through 256 removed outlier: 4.280A pdb=" N LEU B 255 " --> pdb=" O THR B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 298 Proline residue: B 291 - end of helix removed outlier: 3.686A pdb=" N ILE B 294 " --> pdb=" O MET B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 312 removed outlier: 3.920A pdb=" N TYR B 311 " --> pdb=" O VAL B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 340 Processing helix chain 'B' and resid 341 through 344 Processing helix chain 'B' and resid 345 through 360 removed outlier: 3.772A pdb=" N THR B 359 " --> pdb=" O ASN B 355 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY B 360 " --> pdb=" O ILE B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 372 removed outlier: 4.201A pdb=" N TYR B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 11 Processing helix chain 'C' and resid 32 through 54 Proline residue: C 46 - end of helix removed outlier: 3.690A pdb=" N PHE C 54 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 91 removed outlier: 4.443A pdb=" N GLN C 89 " --> pdb=" O TRP C 85 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLN C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 131 Proline residue: C 110 - end of helix Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 158 Processing helix chain 'C' and resid 197 through 207 removed outlier: 3.794A pdb=" N ASN C 207 " --> pdb=" O LYS C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 240 Processing helix chain 'C' and resid 252 through 256 removed outlier: 4.279A pdb=" N LEU C 255 " --> pdb=" O THR C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 298 Proline residue: C 291 - end of helix removed outlier: 3.686A pdb=" N ILE C 294 " --> pdb=" O MET C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 312 removed outlier: 3.920A pdb=" N TYR C 311 " --> pdb=" O VAL C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 340 Processing helix chain 'C' and resid 341 through 344 Processing helix chain 'C' and resid 345 through 360 removed outlier: 3.774A pdb=" N THR C 359 " --> pdb=" O ASN C 355 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY C 360 " --> pdb=" O ILE C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 372 removed outlier: 4.200A pdb=" N TYR C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 11 Processing helix chain 'D' and resid 32 through 54 Proline residue: D 46 - end of helix removed outlier: 3.690A pdb=" N PHE D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 91 removed outlier: 4.442A pdb=" N GLN D 89 " --> pdb=" O TRP D 85 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLN D 90 " --> pdb=" O ALA D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 131 Proline residue: D 110 - end of helix Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 158 Processing helix chain 'D' and resid 197 through 207 removed outlier: 3.794A pdb=" N ASN D 207 " --> pdb=" O LYS D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 240 Processing helix chain 'D' and resid 252 through 256 removed outlier: 4.280A pdb=" N LEU D 255 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 298 Proline residue: D 291 - end of helix removed outlier: 3.686A pdb=" N ILE D 294 " --> pdb=" O MET D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 312 removed outlier: 3.920A pdb=" N TYR D 311 " --> pdb=" O VAL D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 340 Processing helix chain 'D' and resid 341 through 344 Processing helix chain 'D' and resid 345 through 360 removed outlier: 3.773A pdb=" N THR D 359 " --> pdb=" O ASN D 355 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY D 360 " --> pdb=" O ILE D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 372 removed outlier: 4.201A pdb=" N TYR D 368 " --> pdb=" O ASP D 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 11 Processing helix chain 'E' and resid 32 through 54 Proline residue: E 46 - end of helix removed outlier: 3.690A pdb=" N PHE E 54 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 91 removed outlier: 4.442A pdb=" N GLN E 89 " --> pdb=" O TRP E 85 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLN E 90 " --> pdb=" O ALA E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 131 Proline residue: E 110 - end of helix Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 158 Processing helix chain 'E' and resid 197 through 207 removed outlier: 3.795A pdb=" N ASN E 207 " --> pdb=" O LYS E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 240 Processing helix chain 'E' and resid 252 through 256 removed outlier: 4.280A pdb=" N LEU E 255 " --> pdb=" O THR E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 298 Proline residue: E 291 - end of helix removed outlier: 3.687A pdb=" N ILE E 294 " --> pdb=" O MET E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 312 removed outlier: 3.920A pdb=" N TYR E 311 " --> pdb=" O VAL E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 340 Processing helix chain 'E' and resid 341 through 344 Processing helix chain 'E' and resid 345 through 360 removed outlier: 3.773A pdb=" N THR E 359 " --> pdb=" O ASN E 355 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY E 360 " --> pdb=" O ILE E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 372 removed outlier: 4.200A pdb=" N TYR E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 11 Processing helix chain 'F' and resid 32 through 54 Proline residue: F 46 - end of helix removed outlier: 3.690A pdb=" N PHE F 54 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 91 removed outlier: 4.443A pdb=" N GLN F 89 " --> pdb=" O TRP F 85 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN F 90 " --> pdb=" O ALA F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 131 Proline residue: F 110 - end of helix Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 158 Processing helix chain 'F' and resid 197 through 207 removed outlier: 3.795A pdb=" N ASN F 207 " --> pdb=" O LYS F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 240 Processing helix chain 'F' and resid 252 through 256 removed outlier: 4.280A pdb=" N LEU F 255 " --> pdb=" O THR F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 298 Proline residue: F 291 - end of helix removed outlier: 3.686A pdb=" N ILE F 294 " --> pdb=" O MET F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 312 removed outlier: 3.920A pdb=" N TYR F 311 " --> pdb=" O VAL F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 340 Processing helix chain 'F' and resid 341 through 344 Processing helix chain 'F' and resid 345 through 360 removed outlier: 3.774A pdb=" N THR F 359 " --> pdb=" O ASN F 355 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY F 360 " --> pdb=" O ILE F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 372 removed outlier: 4.201A pdb=" N TYR F 368 " --> pdb=" O ASP F 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 11 Processing helix chain 'G' and resid 32 through 54 Proline residue: G 46 - end of helix removed outlier: 3.690A pdb=" N PHE G 54 " --> pdb=" O ILE G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 91 removed outlier: 4.443A pdb=" N GLN G 89 " --> pdb=" O TRP G 85 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLN G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 131 Proline residue: G 110 - end of helix Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 158 Processing helix chain 'G' and resid 197 through 207 removed outlier: 3.796A pdb=" N ASN G 207 " --> pdb=" O LYS G 203 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 240 Processing helix chain 'G' and resid 252 through 256 removed outlier: 4.280A pdb=" N LEU G 255 " --> pdb=" O THR G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 298 Proline residue: G 291 - end of helix removed outlier: 3.686A pdb=" N ILE G 294 " --> pdb=" O MET G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 312 removed outlier: 3.920A pdb=" N TYR G 311 " --> pdb=" O VAL G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 328 through 340 Processing helix chain 'G' and resid 341 through 344 Processing helix chain 'G' and resid 345 through 360 removed outlier: 3.773A pdb=" N THR G 359 " --> pdb=" O ASN G 355 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY G 360 " --> pdb=" O ILE G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 372 removed outlier: 4.201A pdb=" N TYR G 368 " --> pdb=" O ASP G 364 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 66 Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 66 Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 66 1142 hydrogen bonds defined for protein. 3363 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: 2.89 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5383 1.35 - 1.47: 4718 1.47 - 1.58: 8519 1.58 - 1.70: 0 1.70 - 1.82: 98 Bond restraints: 18718 Sorted by residual: bond pdb=" CA VAL A 101 " pdb=" C VAL A 101 " ideal model delta sigma weight residual 1.525 1.551 -0.026 2.10e-02 2.27e+03 1.59e+00 bond pdb=" CA VAL C 101 " pdb=" C VAL C 101 " ideal model delta sigma weight residual 1.525 1.551 -0.026 2.10e-02 2.27e+03 1.59e+00 bond pdb=" CA VAL G 101 " pdb=" C VAL G 101 " ideal model delta sigma weight residual 1.525 1.551 -0.026 2.10e-02 2.27e+03 1.56e+00 bond pdb=" CA VAL B 101 " pdb=" C VAL B 101 " ideal model delta sigma weight residual 1.525 1.550 -0.025 2.10e-02 2.27e+03 1.47e+00 bond pdb=" CA VAL F 101 " pdb=" C VAL F 101 " ideal model delta sigma weight residual 1.525 1.550 -0.025 2.10e-02 2.27e+03 1.47e+00 ... (remaining 18713 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 24846 1.32 - 2.65: 445 2.65 - 3.97: 84 3.97 - 5.29: 56 5.29 - 6.61: 14 Bond angle restraints: 25445 Sorted by residual: angle pdb=" CA VAL B 101 " pdb=" C VAL B 101 " pdb=" N PRO B 102 " ideal model delta sigma weight residual 116.90 120.02 -3.12 1.50e+00 4.44e-01 4.33e+00 angle pdb=" CA VAL F 101 " pdb=" C VAL F 101 " pdb=" N PRO F 102 " ideal model delta sigma weight residual 116.90 120.01 -3.11 1.50e+00 4.44e-01 4.29e+00 angle pdb=" CA VAL C 101 " pdb=" C VAL C 101 " pdb=" N PRO C 102 " ideal model delta sigma weight residual 116.90 119.97 -3.07 1.50e+00 4.44e-01 4.20e+00 angle pdb=" CA VAL D 101 " pdb=" C VAL D 101 " pdb=" N PRO D 102 " ideal model delta sigma weight residual 116.90 119.97 -3.07 1.50e+00 4.44e-01 4.20e+00 angle pdb=" CA VAL E 101 " pdb=" C VAL E 101 " pdb=" N PRO E 102 " ideal model delta sigma weight residual 116.90 119.97 -3.07 1.50e+00 4.44e-01 4.18e+00 ... (remaining 25440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 9609 16.87 - 33.74: 1094 33.74 - 50.61: 378 50.61 - 67.48: 35 67.48 - 84.36: 28 Dihedral angle restraints: 11144 sinusoidal: 4403 harmonic: 6741 Sorted by residual: dihedral pdb=" CB CYS F 84 " pdb=" SG CYS F 84 " pdb=" SG CYS F 248 " pdb=" CB CYS F 248 " ideal model delta sinusoidal sigma weight residual 93.00 15.32 77.68 1 1.00e+01 1.00e-02 7.55e+01 dihedral pdb=" CB CYS E 84 " pdb=" SG CYS E 84 " pdb=" SG CYS E 248 " pdb=" CB CYS E 248 " ideal model delta sinusoidal sigma weight residual 93.00 15.33 77.67 1 1.00e+01 1.00e-02 7.55e+01 dihedral pdb=" CB CYS B 84 " pdb=" SG CYS B 84 " pdb=" SG CYS B 248 " pdb=" CB CYS B 248 " ideal model delta sinusoidal sigma weight residual 93.00 15.33 77.67 1 1.00e+01 1.00e-02 7.55e+01 ... (remaining 11141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2539 0.052 - 0.103: 475 0.103 - 0.155: 24 0.155 - 0.206: 0 0.206 - 0.258: 7 Chirality restraints: 3045 Sorted by residual: chirality pdb=" CB ILE A 217 " pdb=" CA ILE A 217 " pdb=" CG1 ILE A 217 " pdb=" CG2 ILE A 217 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB ILE C 217 " pdb=" CA ILE C 217 " pdb=" CG1 ILE C 217 " pdb=" CG2 ILE C 217 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CB ILE G 217 " pdb=" CA ILE G 217 " pdb=" CG1 ILE G 217 " pdb=" CG2 ILE G 217 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 3042 not shown) Planarity restraints: 3052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 29 " -0.065 9.50e-02 1.11e+02 2.92e-02 6.65e-01 pdb=" NE ARG B 29 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG B 29 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 29 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 29 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 29 " 0.064 9.50e-02 1.11e+02 2.90e-02 6.64e-01 pdb=" NE ARG D 29 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG D 29 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG D 29 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 29 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 29 " 0.064 9.50e-02 1.11e+02 2.88e-02 6.61e-01 pdb=" NE ARG C 29 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG C 29 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG C 29 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 29 " 0.000 2.00e-02 2.50e+03 ... (remaining 3049 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3929 2.78 - 3.31: 17503 3.31 - 3.84: 31206 3.84 - 4.37: 33570 4.37 - 4.90: 61156 Nonbonded interactions: 147364 Sorted by model distance: nonbonded pdb=" OH TYR E 111 " pdb=" O LEU F 52 " model vdw 2.249 3.040 nonbonded pdb=" OH TYR C 111 " pdb=" O LEU D 52 " model vdw 2.249 3.040 nonbonded pdb=" OH TYR D 111 " pdb=" O LEU E 52 " model vdw 2.255 3.040 nonbonded pdb=" OH TYR B 111 " pdb=" O LEU C 52 " model vdw 2.257 3.040 nonbonded pdb=" OH TYR F 111 " pdb=" O LEU G 52 " model vdw 2.258 3.040 ... (remaining 147359 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: 0.06 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 13.480 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 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 : 0.002 0.026 18732 Z= 0.109 Angle : 0.534 7.439 25473 Z= 0.268 Chirality : 0.038 0.258 3045 Planarity : 0.003 0.029 3052 Dihedral : 16.193 84.356 6720 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.73 % Allowed : 22.53 % Favored : 74.74 % 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: 2.18 (0.18), residues: 2198 helix: 2.54 (0.13), residues: 1505 sheet: 0.26 (0.47), residues: 91 loop : -1.34 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 29 TYR 0.006 0.001 TYR A 232 PHE 0.008 0.001 PHE B 12 TRP 0.008 0.001 TRP A 74 HIS 0.001 0.000 HIS C 106 Details of bonding type rmsd covalent geometry : bond 0.00218 (18718) covalent geometry : angle 0.51221 (25445) SS BOND : bond 0.00115 ( 14) SS BOND : angle 4.56803 ( 28) hydrogen bonds : bond 0.09457 ( 1142) hydrogen bonds : angle 4.15936 ( 3363) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 389 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 ARG cc_start: 0.6923 (ptm-80) cc_final: 0.6338 (mtm110) REVERT: A 354 GLU cc_start: 0.8961 (tp30) cc_final: 0.8484 (tp30) REVERT: A 358 ASN cc_start: 0.8702 (t0) cc_final: 0.8397 (t0) REVERT: B 152 ARG cc_start: 0.6669 (ptm-80) cc_final: 0.6132 (mtm110) REVERT: B 354 GLU cc_start: 0.8884 (tp30) cc_final: 0.8602 (tp30) REVERT: B 358 ASN cc_start: 0.8710 (t0) cc_final: 0.8374 (t0) REVERT: C 14 ASP cc_start: 0.8010 (m-30) cc_final: 0.7778 (p0) REVERT: C 152 ARG cc_start: 0.6764 (ptm-80) cc_final: 0.6278 (mtm110) REVERT: C 354 GLU cc_start: 0.8941 (tp30) cc_final: 0.8694 (tp30) REVERT: D 152 ARG cc_start: 0.6761 (ptm-80) cc_final: 0.6240 (mtm110) REVERT: D 240 PHE cc_start: 0.7038 (OUTLIER) cc_final: 0.5983 (m-80) REVERT: D 354 GLU cc_start: 0.8943 (tp30) cc_final: 0.8691 (tp30) REVERT: E 152 ARG cc_start: 0.6982 (ptm-80) cc_final: 0.6399 (mtm110) REVERT: E 354 GLU cc_start: 0.8967 (tp30) cc_final: 0.8702 (tp30) REVERT: F 152 ARG cc_start: 0.6876 (ptm-80) cc_final: 0.6446 (mtm110) REVERT: F 354 GLU cc_start: 0.8969 (tp30) cc_final: 0.8553 (tp30) REVERT: F 358 ASN cc_start: 0.8695 (t0) cc_final: 0.8446 (t0) REVERT: G 152 ARG cc_start: 0.6832 (ptm-80) cc_final: 0.6232 (mtm110) REVERT: G 354 GLU cc_start: 0.9005 (tp30) cc_final: 0.8740 (tp30) outliers start: 56 outliers final: 19 residues processed: 416 average time/residue: 0.6536 time to fit residues: 301.1516 Evaluate side-chains 270 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 250 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 124 ASN Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 124 ASN Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 124 ASN Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 240 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.0470 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 overall best weight: 1.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 355 ASN B 56 GLN B 266 GLN B 282 ASN B 355 ASN C 266 GLN C 355 ASN D 266 GLN D 355 ASN E 266 GLN E 355 ASN F 266 GLN F 355 ASN G 56 GLN G 266 GLN G 355 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.128437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.087157 restraints weight = 30736.672| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.45 r_work: 0.3001 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 18732 Z= 0.147 Angle : 0.601 7.672 25473 Z= 0.291 Chirality : 0.039 0.197 3045 Planarity : 0.003 0.032 3052 Dihedral : 4.346 48.896 2451 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 5.70 % Allowed : 23.55 % Favored : 70.75 % 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: 2.23 (0.19), residues: 2198 helix: 2.50 (0.13), residues: 1533 sheet: -0.29 (0.45), residues: 126 loop : -1.22 (0.29), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 29 TYR 0.020 0.001 TYR A 232 PHE 0.009 0.001 PHE G 240 TRP 0.007 0.001 TRP C 127 HIS 0.003 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00352 (18718) covalent geometry : angle 0.59841 (25445) SS BOND : bond 0.00111 ( 14) SS BOND : angle 1.88177 ( 28) hydrogen bonds : bond 0.03578 ( 1142) hydrogen bonds : angle 3.74185 ( 3363) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 264 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8348 (m-30) cc_final: 0.7929 (t0) REVERT: A 144 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.8006 (mp0) REVERT: A 152 ARG cc_start: 0.6153 (ptm-80) cc_final: 0.5723 (mtm110) REVERT: A 240 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.6446 (m-80) REVERT: A 358 ASN cc_start: 0.8772 (t0) cc_final: 0.8441 (t0) REVERT: B 14 ASP cc_start: 0.8661 (m-30) cc_final: 0.7777 (p0) REVERT: B 144 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: B 152 ARG cc_start: 0.6107 (ptm-80) cc_final: 0.5674 (mtm110) REVERT: B 306 ASN cc_start: 0.7398 (t0) cc_final: 0.6981 (t0) REVERT: B 358 ASN cc_start: 0.8786 (t0) cc_final: 0.8396 (t0) REVERT: C 14 ASP cc_start: 0.8554 (m-30) cc_final: 0.7733 (p0) REVERT: C 152 ARG cc_start: 0.5988 (ptm-80) cc_final: 0.5634 (mtm110) REVERT: D 152 ARG cc_start: 0.6123 (ptm-80) cc_final: 0.5661 (mtm110) REVERT: E 14 ASP cc_start: 0.8536 (m-30) cc_final: 0.7910 (p0) REVERT: E 144 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7881 (mp0) REVERT: E 152 ARG cc_start: 0.6127 (ptm-80) cc_final: 0.5608 (mtm110) REVERT: E 200 GLN cc_start: 0.8879 (mm-40) cc_final: 0.8256 (mm-40) REVERT: E 258 ASP cc_start: 0.8835 (t0) cc_final: 0.8561 (t0) REVERT: E 297 MET cc_start: 0.7769 (pmm) cc_final: 0.7533 (pmm) REVERT: E 306 ASN cc_start: 0.7558 (t0) cc_final: 0.7180 (t0) REVERT: F 14 ASP cc_start: 0.8464 (m-30) cc_final: 0.7781 (t70) REVERT: F 152 ARG cc_start: 0.6164 (ptm-80) cc_final: 0.5894 (mtp-110) REVERT: F 358 ASN cc_start: 0.8792 (t0) cc_final: 0.8515 (t0) REVERT: G 14 ASP cc_start: 0.8479 (m-30) cc_final: 0.7812 (p0) REVERT: G 144 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7871 (mp0) REVERT: G 152 ARG cc_start: 0.6078 (ptm-80) cc_final: 0.5590 (mtm110) outliers start: 117 outliers final: 34 residues processed: 355 average time/residue: 0.5209 time to fit residues: 209.1048 Evaluate side-chains 291 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 252 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 124 ASN Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 352 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 75 optimal weight: 6.9990 chunk 192 optimal weight: 8.9990 chunk 22 optimal weight: 0.6980 chunk 206 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 33 optimal weight: 0.1980 chunk 223 optimal weight: 20.0000 chunk 154 optimal weight: 7.9990 chunk 130 optimal weight: 20.0000 chunk 66 optimal weight: 9.9990 chunk 176 optimal weight: 4.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 340 ASN B 56 GLN B 355 ASN C 266 GLN C 355 ASN ** D 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 ASN E 355 ASN F 56 GLN F 340 ASN F 355 ASN G 355 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.124104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.081588 restraints weight = 31042.965| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.46 r_work: 0.2906 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 18732 Z= 0.225 Angle : 0.647 9.166 25473 Z= 0.315 Chirality : 0.042 0.190 3045 Planarity : 0.003 0.030 3052 Dihedral : 3.994 50.879 2432 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 5.80 % Allowed : 23.94 % Favored : 70.26 % 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: 1.85 (0.19), residues: 2198 helix: 2.23 (0.13), residues: 1519 sheet: -0.02 (0.48), residues: 126 loop : -1.39 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 29 TYR 0.037 0.002 TYR A 232 PHE 0.010 0.002 PHE E 333 TRP 0.012 0.002 TRP F 85 HIS 0.005 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00552 (18718) covalent geometry : angle 0.64480 (25445) SS BOND : bond 0.00081 ( 14) SS BOND : angle 1.87849 ( 28) hydrogen bonds : bond 0.04139 ( 1142) hydrogen bonds : angle 3.91277 ( 3363) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 248 time to evaluate : 0.681 Fit side-chains REVERT: A 14 ASP cc_start: 0.8465 (m-30) cc_final: 0.8004 (t0) REVERT: A 56 GLN cc_start: 0.8904 (mm-40) cc_final: 0.8692 (mm-40) REVERT: A 124 ASN cc_start: 0.8193 (OUTLIER) cc_final: 0.7925 (p0) REVERT: A 144 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8066 (mp0) REVERT: A 152 ARG cc_start: 0.6263 (ptm-80) cc_final: 0.5808 (mtm110) REVERT: A 240 PHE cc_start: 0.7703 (OUTLIER) cc_final: 0.7174 (m-80) REVERT: A 306 ASN cc_start: 0.7521 (t0) cc_final: 0.7304 (t0) REVERT: A 358 ASN cc_start: 0.8816 (t0) cc_final: 0.8480 (t0) REVERT: B 14 ASP cc_start: 0.8637 (m-30) cc_final: 0.7841 (p0) REVERT: B 144 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8034 (mp0) REVERT: B 152 ARG cc_start: 0.6151 (ptm-80) cc_final: 0.5751 (mtm110) REVERT: B 240 PHE cc_start: 0.7644 (OUTLIER) cc_final: 0.7331 (m-80) REVERT: B 266 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8216 (tt0) REVERT: B 317 PHE cc_start: 0.7830 (t80) cc_final: 0.7365 (m-80) REVERT: B 358 ASN cc_start: 0.8839 (t0) cc_final: 0.8458 (t0) REVERT: C 14 ASP cc_start: 0.8568 (m-30) cc_final: 0.7829 (p0) REVERT: C 124 ASN cc_start: 0.8300 (OUTLIER) cc_final: 0.7986 (p0) REVERT: C 144 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.8034 (mp0) REVERT: C 152 ARG cc_start: 0.6043 (ptm-80) cc_final: 0.5657 (mtm110) REVERT: C 297 MET cc_start: 0.8079 (pmm) cc_final: 0.7617 (pmm) REVERT: C 306 ASN cc_start: 0.7642 (t0) cc_final: 0.7406 (t0) REVERT: D 14 ASP cc_start: 0.8320 (m-30) cc_final: 0.7596 (p0) REVERT: D 124 ASN cc_start: 0.8239 (OUTLIER) cc_final: 0.7959 (p0) REVERT: D 152 ARG cc_start: 0.6167 (ptm-80) cc_final: 0.5702 (mtm110) REVERT: D 266 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8508 (tt0) REVERT: D 306 ASN cc_start: 0.7457 (t0) cc_final: 0.7238 (t0) REVERT: E 14 ASP cc_start: 0.8527 (m-30) cc_final: 0.7814 (p0) REVERT: E 144 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7917 (mp0) REVERT: E 152 ARG cc_start: 0.6206 (ptm-80) cc_final: 0.5809 (mtm110) REVERT: E 203 LYS cc_start: 0.9290 (mmmt) cc_final: 0.8869 (mmtt) REVERT: E 266 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8197 (tt0) REVERT: E 297 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7645 (pmm) REVERT: E 306 ASN cc_start: 0.7572 (t0) cc_final: 0.7339 (t0) REVERT: F 14 ASP cc_start: 0.8590 (m-30) cc_final: 0.7879 (t0) REVERT: F 144 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8196 (mp0) REVERT: F 266 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8265 (tt0) REVERT: F 338 GLU cc_start: 0.8922 (tt0) cc_final: 0.8411 (tp30) REVERT: F 354 GLU cc_start: 0.9045 (tp30) cc_final: 0.8637 (tp30) REVERT: F 358 ASN cc_start: 0.8867 (t0) cc_final: 0.8610 (t0) REVERT: G 14 ASP cc_start: 0.8527 (m-30) cc_final: 0.7822 (p0) REVERT: G 29 ARG cc_start: 0.8866 (mtm-85) cc_final: 0.8570 (mtt180) REVERT: G 128 ARG cc_start: 0.8670 (tmm-80) cc_final: 0.8399 (ttt-90) REVERT: G 144 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: G 152 ARG cc_start: 0.6121 (ptm-80) cc_final: 0.5637 (mtm110) REVERT: G 266 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8284 (tt0) REVERT: G 276 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8274 (mtp-110) REVERT: G 306 ASN cc_start: 0.7444 (t0) cc_final: 0.7214 (t0) outliers start: 119 outliers final: 48 residues processed: 343 average time/residue: 0.5323 time to fit residues: 206.4731 Evaluate side-chains 295 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 230 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 124 ASN Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 266 GLN Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 276 ARG Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain E residue 124 ASN Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 124 ASN Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 266 GLN Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 266 GLN Chi-restraints excluded: chain G residue 276 ARG Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 352 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 7 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 57 optimal weight: 7.9990 chunk 66 optimal weight: 0.0020 chunk 31 optimal weight: 20.0000 chunk 77 optimal weight: 4.9990 chunk 158 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 ASN C 266 GLN C 355 ASN D 340 ASN D 355 ASN E 355 ASN F 340 ASN F 355 ASN G 56 GLN G 355 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.125419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.083711 restraints weight = 30814.453| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.44 r_work: 0.2943 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18732 Z= 0.141 Angle : 0.604 8.805 25473 Z= 0.289 Chirality : 0.040 0.181 3045 Planarity : 0.003 0.028 3052 Dihedral : 3.990 52.239 2431 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 5.80 % Allowed : 22.96 % Favored : 71.23 % 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: 2.00 (0.19), residues: 2198 helix: 2.34 (0.13), residues: 1519 sheet: 0.04 (0.48), residues: 126 loop : -1.35 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 29 TYR 0.024 0.001 TYR E 232 PHE 0.010 0.001 PHE D 12 TRP 0.007 0.001 TRP F 85 HIS 0.003 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00337 (18718) covalent geometry : angle 0.60169 (25445) SS BOND : bond 0.00142 ( 14) SS BOND : angle 1.59279 ( 28) hydrogen bonds : bond 0.03633 ( 1142) hydrogen bonds : angle 3.78235 ( 3363) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 245 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8512 (m-30) cc_final: 0.7984 (t0) REVERT: A 124 ASN cc_start: 0.8121 (OUTLIER) cc_final: 0.7878 (p0) REVERT: A 144 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.8002 (mp0) REVERT: A 152 ARG cc_start: 0.6274 (ptm-80) cc_final: 0.5824 (mtm110) REVERT: A 240 PHE cc_start: 0.7718 (OUTLIER) cc_final: 0.7173 (m-80) REVERT: A 306 ASN cc_start: 0.7517 (t0) cc_final: 0.7270 (t0) REVERT: A 358 ASN cc_start: 0.8833 (t0) cc_final: 0.8489 (t0) REVERT: B 14 ASP cc_start: 0.8594 (m-30) cc_final: 0.7801 (p0) REVERT: B 124 ASN cc_start: 0.8348 (OUTLIER) cc_final: 0.8040 (p0) REVERT: B 144 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7999 (mp0) REVERT: B 152 ARG cc_start: 0.6158 (ptm-80) cc_final: 0.5716 (mtm110) REVERT: B 203 LYS cc_start: 0.9219 (mmmt) cc_final: 0.8812 (mmtt) REVERT: B 240 PHE cc_start: 0.7638 (OUTLIER) cc_final: 0.7355 (m-80) REVERT: B 266 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8167 (tt0) REVERT: B 306 ASN cc_start: 0.7559 (t0) cc_final: 0.7319 (t0) REVERT: B 317 PHE cc_start: 0.7774 (t80) cc_final: 0.7344 (m-80) REVERT: B 358 ASN cc_start: 0.8845 (t0) cc_final: 0.8449 (t0) REVERT: C 14 ASP cc_start: 0.8532 (m-30) cc_final: 0.7827 (p0) REVERT: C 124 ASN cc_start: 0.8290 (OUTLIER) cc_final: 0.7993 (p0) REVERT: C 152 ARG cc_start: 0.6050 (ptm-80) cc_final: 0.5683 (mtm110) REVERT: C 200 GLN cc_start: 0.8600 (mm-40) cc_final: 0.8383 (mm-40) REVERT: C 297 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7564 (pmm) REVERT: C 306 ASN cc_start: 0.7619 (t0) cc_final: 0.7388 (t0) REVERT: D 14 ASP cc_start: 0.8305 (m-30) cc_final: 0.7581 (p0) REVERT: D 124 ASN cc_start: 0.8252 (OUTLIER) cc_final: 0.7983 (p0) REVERT: D 152 ARG cc_start: 0.6187 (ptm-80) cc_final: 0.5743 (mtm110) REVERT: D 306 ASN cc_start: 0.7497 (t0) cc_final: 0.7249 (t0) REVERT: E 14 ASP cc_start: 0.8502 (m-30) cc_final: 0.7786 (p0) REVERT: E 144 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7925 (mp0) REVERT: E 152 ARG cc_start: 0.6240 (ptm-80) cc_final: 0.5837 (mtm110) REVERT: E 203 LYS cc_start: 0.9298 (mmmt) cc_final: 0.8870 (mmtt) REVERT: E 266 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8071 (tt0) REVERT: E 297 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7582 (pmm) REVERT: E 306 ASN cc_start: 0.7574 (t0) cc_final: 0.7307 (t0) REVERT: F 14 ASP cc_start: 0.8577 (m-30) cc_final: 0.7858 (t0) REVERT: F 124 ASN cc_start: 0.8151 (OUTLIER) cc_final: 0.7813 (p0) REVERT: F 203 LYS cc_start: 0.9186 (mmmt) cc_final: 0.8836 (mptt) REVERT: F 358 ASN cc_start: 0.8899 (t0) cc_final: 0.8628 (t0) REVERT: G 14 ASP cc_start: 0.8491 (m-30) cc_final: 0.7706 (p0) REVERT: G 29 ARG cc_start: 0.8889 (mtm-85) cc_final: 0.8632 (mtt180) REVERT: G 128 ARG cc_start: 0.8665 (tmm-80) cc_final: 0.8354 (ttt180) REVERT: G 144 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7837 (mp0) REVERT: G 152 ARG cc_start: 0.6244 (ptm-80) cc_final: 0.5722 (mtm110) REVERT: G 200 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8370 (mm-40) REVERT: G 276 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.8160 (mtp-110) REVERT: G 306 ASN cc_start: 0.7387 (t0) cc_final: 0.7154 (t0) outliers start: 119 outliers final: 54 residues processed: 338 average time/residue: 0.5196 time to fit residues: 199.7254 Evaluate side-chains 305 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 235 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 124 ASN Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 276 ARG Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 124 ASN Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 124 ASN Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 276 ARG Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 352 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 6 optimal weight: 0.0670 chunk 190 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 141 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 overall best weight: 2.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN B 355 ASN C 266 GLN C 355 ASN D 355 ASN E 355 ASN F 282 ASN F 340 ASN G 56 GLN G 282 ASN G 355 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.124110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.081651 restraints weight = 30818.215| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.46 r_work: 0.2910 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 18732 Z= 0.187 Angle : 0.636 9.339 25473 Z= 0.305 Chirality : 0.041 0.204 3045 Planarity : 0.003 0.027 3052 Dihedral : 3.855 52.907 2428 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 6.09 % Allowed : 22.96 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.19), residues: 2198 helix: 2.23 (0.13), residues: 1519 sheet: 0.24 (0.49), residues: 126 loop : -1.42 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 29 TYR 0.029 0.002 TYR E 232 PHE 0.010 0.001 PHE F 333 TRP 0.011 0.002 TRP F 85 HIS 0.004 0.001 HIS C 106 Details of bonding type rmsd covalent geometry : bond 0.00457 (18718) covalent geometry : angle 0.63432 (25445) SS BOND : bond 0.00116 ( 14) SS BOND : angle 1.51737 ( 28) hydrogen bonds : bond 0.03891 ( 1142) hydrogen bonds : angle 3.86439 ( 3363) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 237 time to evaluate : 0.744 Fit side-chains REVERT: A 14 ASP cc_start: 0.8671 (m-30) cc_final: 0.7701 (p0) REVERT: A 124 ASN cc_start: 0.8311 (OUTLIER) cc_final: 0.8045 (p0) REVERT: A 144 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8168 (mp0) REVERT: A 152 ARG cc_start: 0.6301 (ptm-80) cc_final: 0.5842 (mtm110) REVERT: A 240 PHE cc_start: 0.7959 (OUTLIER) cc_final: 0.7551 (m-80) REVERT: A 306 ASN cc_start: 0.7577 (t0) cc_final: 0.7319 (t0) REVERT: A 358 ASN cc_start: 0.8862 (t0) cc_final: 0.8525 (t0) REVERT: B 14 ASP cc_start: 0.8696 (m-30) cc_final: 0.7875 (p0) REVERT: B 124 ASN cc_start: 0.8472 (OUTLIER) cc_final: 0.8163 (p0) REVERT: B 144 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8168 (mp0) REVERT: B 152 ARG cc_start: 0.6290 (ptm-80) cc_final: 0.5826 (mtm110) REVERT: B 240 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.7532 (m-80) REVERT: B 266 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8380 (tt0) REVERT: B 306 ASN cc_start: 0.7550 (t0) cc_final: 0.7263 (t0) REVERT: B 317 PHE cc_start: 0.7817 (t80) cc_final: 0.7348 (m-80) REVERT: B 358 ASN cc_start: 0.8868 (t0) cc_final: 0.8493 (t0) REVERT: C 14 ASP cc_start: 0.8639 (m-30) cc_final: 0.7864 (p0) REVERT: C 124 ASN cc_start: 0.8350 (OUTLIER) cc_final: 0.8024 (p0) REVERT: C 144 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8125 (mp0) REVERT: C 152 ARG cc_start: 0.6135 (ptm-80) cc_final: 0.5729 (mtm110) REVERT: C 297 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.8066 (pmm) REVERT: C 306 ASN cc_start: 0.7580 (t0) cc_final: 0.7343 (t0) REVERT: D 14 ASP cc_start: 0.8481 (m-30) cc_final: 0.7676 (p0) REVERT: D 124 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.8094 (p0) REVERT: D 144 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8388 (mp0) REVERT: D 152 ARG cc_start: 0.6147 (ptm-80) cc_final: 0.5678 (mtm110) REVERT: D 306 ASN cc_start: 0.7646 (t0) cc_final: 0.7372 (t0) REVERT: D 317 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7616 (m-80) REVERT: E 14 ASP cc_start: 0.8628 (m-30) cc_final: 0.7878 (p0) REVERT: E 88 VAL cc_start: 0.8368 (OUTLIER) cc_final: 0.8165 (p) REVERT: E 144 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8091 (mp0) REVERT: E 152 ARG cc_start: 0.6279 (ptm-80) cc_final: 0.5881 (mtm110) REVERT: E 203 LYS cc_start: 0.9288 (mmmt) cc_final: 0.8848 (mmtt) REVERT: E 266 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8301 (tt0) REVERT: E 297 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7644 (pmm) REVERT: E 306 ASN cc_start: 0.7636 (t0) cc_final: 0.7326 (t0) REVERT: F 14 ASP cc_start: 0.8703 (m-30) cc_final: 0.7848 (p0) REVERT: F 144 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8344 (mp0) REVERT: F 203 LYS cc_start: 0.9239 (mmmt) cc_final: 0.8884 (mptt) REVERT: F 266 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8397 (tt0) REVERT: F 358 ASN cc_start: 0.8945 (t0) cc_final: 0.8689 (t0) REVERT: G 14 ASP cc_start: 0.8708 (m-30) cc_final: 0.7829 (p0) REVERT: G 88 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.8298 (p) REVERT: G 128 ARG cc_start: 0.8759 (tmm-80) cc_final: 0.8500 (ttt180) REVERT: G 144 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8019 (mp0) REVERT: G 152 ARG cc_start: 0.6242 (ptm-80) cc_final: 0.5704 (mtm110) REVERT: G 200 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8502 (mm-40) REVERT: G 203 LYS cc_start: 0.9261 (mmmt) cc_final: 0.8851 (mmtt) REVERT: G 276 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8414 (mtp-110) REVERT: G 306 ASN cc_start: 0.7568 (t0) cc_final: 0.7332 (t0) outliers start: 125 outliers final: 65 residues processed: 335 average time/residue: 0.5341 time to fit residues: 202.8085 Evaluate side-chains 318 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 233 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 124 ASN Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 276 ARG Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 317 PHE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 124 ASN Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 124 ASN Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 266 GLN Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 276 ARG Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 352 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 42 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 221 optimal weight: 9.9990 chunk 33 optimal weight: 0.0470 chunk 125 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 178 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN A 355 ASN B 56 GLN B 355 ASN C 266 GLN C 355 ASN D 340 ASN D 355 ASN E 355 ASN F 282 ASN F 340 ASN G 355 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.126346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.084515 restraints weight = 30400.837| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.45 r_work: 0.2964 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18732 Z= 0.118 Angle : 0.604 8.297 25473 Z= 0.288 Chirality : 0.039 0.184 3045 Planarity : 0.003 0.030 3052 Dihedral : 3.833 54.159 2428 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 5.31 % Allowed : 23.21 % Favored : 71.48 % 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: 2.10 (0.19), residues: 2198 helix: 2.41 (0.14), residues: 1512 sheet: 0.28 (0.48), residues: 126 loop : -1.30 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 29 TYR 0.027 0.001 TYR E 232 PHE 0.011 0.001 PHE D 12 TRP 0.005 0.001 TRP A 104 HIS 0.002 0.001 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00265 (18718) covalent geometry : angle 0.60258 (25445) SS BOND : bond 0.00231 ( 14) SS BOND : angle 1.49038 ( 28) hydrogen bonds : bond 0.03438 ( 1142) hydrogen bonds : angle 3.71886 ( 3363) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 254 time to evaluate : 0.740 Fit side-chains REVERT: A 14 ASP cc_start: 0.8612 (m-30) cc_final: 0.7679 (p0) REVERT: A 124 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.8015 (p0) REVERT: A 144 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8100 (mp0) REVERT: A 152 ARG cc_start: 0.6298 (ptm-80) cc_final: 0.5798 (mtm110) REVERT: A 240 PHE cc_start: 0.7846 (OUTLIER) cc_final: 0.7338 (m-80) REVERT: A 306 ASN cc_start: 0.7575 (t0) cc_final: 0.7312 (t0) REVERT: A 358 ASN cc_start: 0.8872 (t0) cc_final: 0.8535 (t0) REVERT: B 14 ASP cc_start: 0.8648 (m-30) cc_final: 0.7865 (p0) REVERT: B 124 ASN cc_start: 0.8490 (OUTLIER) cc_final: 0.8201 (p0) REVERT: B 144 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8131 (mp0) REVERT: B 152 ARG cc_start: 0.6311 (ptm-80) cc_final: 0.5830 (mtm110) REVERT: B 240 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.7500 (m-80) REVERT: B 266 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8270 (tt0) REVERT: B 306 ASN cc_start: 0.7580 (t0) cc_final: 0.7281 (t0) REVERT: B 317 PHE cc_start: 0.7752 (t80) cc_final: 0.7329 (m-80) REVERT: B 358 ASN cc_start: 0.8861 (t0) cc_final: 0.8505 (t0) REVERT: C 14 ASP cc_start: 0.8597 (m-30) cc_final: 0.7774 (p0) REVERT: C 124 ASN cc_start: 0.8344 (OUTLIER) cc_final: 0.8001 (p0) REVERT: C 144 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8076 (mp0) REVERT: C 152 ARG cc_start: 0.6132 (ptm-80) cc_final: 0.5656 (mtm110) REVERT: C 200 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8356 (mm-40) REVERT: C 306 ASN cc_start: 0.7694 (t0) cc_final: 0.7454 (t0) REVERT: D 14 ASP cc_start: 0.8451 (m-30) cc_final: 0.7659 (p0) REVERT: D 124 ASN cc_start: 0.8389 (OUTLIER) cc_final: 0.8026 (p0) REVERT: D 152 ARG cc_start: 0.6334 (ptm-80) cc_final: 0.5828 (mtm110) REVERT: D 306 ASN cc_start: 0.7656 (t0) cc_final: 0.7342 (t0) REVERT: D 317 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7588 (m-80) REVERT: E 14 ASP cc_start: 0.8585 (m-30) cc_final: 0.7857 (p0) REVERT: E 144 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8112 (mp0) REVERT: E 152 ARG cc_start: 0.6330 (ptm-80) cc_final: 0.5877 (mtm110) REVERT: E 203 LYS cc_start: 0.9251 (mmmt) cc_final: 0.8903 (mptt) REVERT: E 297 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7636 (pmm) REVERT: E 306 ASN cc_start: 0.7639 (t0) cc_final: 0.7335 (t0) REVERT: F 14 ASP cc_start: 0.8669 (m-30) cc_final: 0.8011 (t0) REVERT: F 124 ASN cc_start: 0.8253 (OUTLIER) cc_final: 0.7893 (p0) REVERT: F 144 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8367 (mp0) REVERT: F 203 LYS cc_start: 0.9211 (mmmt) cc_final: 0.8851 (mptt) REVERT: F 232 TYR cc_start: 0.7929 (t80) cc_final: 0.7591 (t80) REVERT: F 280 TYR cc_start: 0.8372 (t80) cc_final: 0.7738 (m-80) REVERT: F 297 MET cc_start: 0.8081 (pmt) cc_final: 0.7821 (pmt) REVERT: F 358 ASN cc_start: 0.8980 (t0) cc_final: 0.8708 (t0) REVERT: G 14 ASP cc_start: 0.8572 (m-30) cc_final: 0.7765 (p0) REVERT: G 128 ARG cc_start: 0.8684 (tmm-80) cc_final: 0.8448 (ttt180) REVERT: G 144 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7964 (mp0) REVERT: G 152 ARG cc_start: 0.6246 (ptm-80) cc_final: 0.5717 (mtm110) REVERT: G 200 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8479 (mm-40) REVERT: G 203 LYS cc_start: 0.9228 (mmmt) cc_final: 0.8821 (mmtt) REVERT: G 266 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8394 (tt0) REVERT: G 306 ASN cc_start: 0.7592 (t0) cc_final: 0.7359 (t0) outliers start: 109 outliers final: 49 residues processed: 337 average time/residue: 0.5433 time to fit residues: 208.3846 Evaluate side-chains 309 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 244 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 124 ASN Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 276 ARG Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 317 PHE Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 124 ASN Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 124 ASN Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 266 GLN Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 352 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 214 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 188 optimal weight: 5.9990 chunk 174 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 170 optimal weight: 3.9990 chunk 126 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 56 GLN B 355 ASN C 355 ASN D 355 ASN E 355 ASN F 282 ASN F 340 ASN G 56 GLN G 355 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.124068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.081868 restraints weight = 30735.750| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.45 r_work: 0.2915 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 18732 Z= 0.185 Angle : 0.656 12.533 25473 Z= 0.313 Chirality : 0.041 0.205 3045 Planarity : 0.003 0.028 3052 Dihedral : 3.826 54.137 2426 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.97 % Allowed : 24.18 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.19), residues: 2198 helix: 2.23 (0.14), residues: 1519 sheet: 0.39 (0.49), residues: 126 loop : -1.37 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 29 TYR 0.031 0.002 TYR E 232 PHE 0.015 0.001 PHE A 333 TRP 0.010 0.002 TRP D 85 HIS 0.005 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00454 (18718) covalent geometry : angle 0.65419 (25445) SS BOND : bond 0.00141 ( 14) SS BOND : angle 1.55091 ( 28) hydrogen bonds : bond 0.03856 ( 1142) hydrogen bonds : angle 3.85454 ( 3363) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 246 time to evaluate : 0.759 Fit side-chains REVERT: A 14 ASP cc_start: 0.8645 (m-30) cc_final: 0.7705 (p0) REVERT: A 124 ASN cc_start: 0.8337 (OUTLIER) cc_final: 0.8035 (p0) REVERT: A 144 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8145 (mp0) REVERT: A 152 ARG cc_start: 0.6296 (ptm-80) cc_final: 0.5762 (mtm110) REVERT: A 240 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7519 (m-80) REVERT: A 306 ASN cc_start: 0.7542 (t0) cc_final: 0.7264 (t0) REVERT: A 317 PHE cc_start: 0.7938 (t80) cc_final: 0.7701 (m-80) REVERT: A 358 ASN cc_start: 0.8889 (t0) cc_final: 0.8537 (t0) REVERT: B 14 ASP cc_start: 0.8631 (m-30) cc_final: 0.7851 (p0) REVERT: B 124 ASN cc_start: 0.8494 (OUTLIER) cc_final: 0.8180 (p0) REVERT: B 144 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8125 (mp0) REVERT: B 152 ARG cc_start: 0.6323 (ptm-80) cc_final: 0.5821 (mtm110) REVERT: B 240 PHE cc_start: 0.7845 (OUTLIER) cc_final: 0.7548 (m-80) REVERT: B 266 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8392 (tt0) REVERT: B 306 ASN cc_start: 0.7640 (t0) cc_final: 0.7347 (t0) REVERT: B 317 PHE cc_start: 0.7827 (t80) cc_final: 0.7362 (m-80) REVERT: B 358 ASN cc_start: 0.8867 (t0) cc_final: 0.8515 (t0) REVERT: C 14 ASP cc_start: 0.8626 (m-30) cc_final: 0.7786 (p0) REVERT: C 124 ASN cc_start: 0.8362 (OUTLIER) cc_final: 0.8021 (p0) REVERT: C 144 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8117 (mp0) REVERT: C 152 ARG cc_start: 0.6162 (ptm-80) cc_final: 0.5677 (mtm110) REVERT: C 255 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8726 (pp) REVERT: C 306 ASN cc_start: 0.7603 (t0) cc_final: 0.7385 (t0) REVERT: D 14 ASP cc_start: 0.8469 (m-30) cc_final: 0.7643 (p0) REVERT: D 124 ASN cc_start: 0.8318 (OUTLIER) cc_final: 0.7865 (p0) REVERT: D 152 ARG cc_start: 0.6281 (ptm-80) cc_final: 0.5790 (mtm110) REVERT: D 306 ASN cc_start: 0.7712 (t0) cc_final: 0.7396 (t0) REVERT: D 317 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7537 (m-80) REVERT: E 14 ASP cc_start: 0.8582 (m-30) cc_final: 0.7847 (p0) REVERT: E 144 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: E 152 ARG cc_start: 0.6329 (ptm-80) cc_final: 0.5885 (mtm110) REVERT: E 203 LYS cc_start: 0.9262 (mmmt) cc_final: 0.8921 (mptt) REVERT: E 266 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8285 (tt0) REVERT: E 297 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7652 (pmm) REVERT: E 306 ASN cc_start: 0.7639 (t0) cc_final: 0.7316 (t0) REVERT: F 14 ASP cc_start: 0.8667 (m-30) cc_final: 0.7839 (p0) REVERT: F 144 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8363 (mp0) REVERT: F 203 LYS cc_start: 0.9251 (mmmt) cc_final: 0.8905 (mptt) REVERT: F 280 TYR cc_start: 0.8374 (t80) cc_final: 0.7731 (m-80) REVERT: F 297 MET cc_start: 0.8135 (pmt) cc_final: 0.7873 (pmt) REVERT: F 358 ASN cc_start: 0.8999 (t0) cc_final: 0.8721 (t0) REVERT: F 374 THR cc_start: 0.8806 (p) cc_final: 0.8595 (t) REVERT: G 14 ASP cc_start: 0.8628 (m-30) cc_final: 0.7800 (p0) REVERT: G 144 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: G 152 ARG cc_start: 0.6260 (ptm-80) cc_final: 0.5737 (mtm110) REVERT: G 200 GLN cc_start: 0.8733 (mm-40) cc_final: 0.8507 (mm-40) REVERT: G 203 LYS cc_start: 0.9240 (mmmt) cc_final: 0.8831 (mmtt) REVERT: G 266 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8412 (tt0) REVERT: G 306 ASN cc_start: 0.7636 (t0) cc_final: 0.7403 (t0) outliers start: 102 outliers final: 55 residues processed: 325 average time/residue: 0.5513 time to fit residues: 203.0089 Evaluate side-chains 310 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 238 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 124 ASN Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 276 ARG Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 317 PHE Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 124 ASN Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 124 ASN Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 266 GLN Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 352 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 138 optimal weight: 0.7980 chunk 221 optimal weight: 0.6980 chunk 139 optimal weight: 0.7980 chunk 223 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 171 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 355 ASN C 355 ASN D 355 ASN E 355 ASN F 340 ASN G 56 GLN G 355 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.125592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.083714 restraints weight = 30500.513| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.44 r_work: 0.2948 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18732 Z= 0.135 Angle : 0.641 12.126 25473 Z= 0.304 Chirality : 0.040 0.204 3045 Planarity : 0.003 0.031 3052 Dihedral : 3.851 56.045 2426 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.68 % Allowed : 24.72 % Favored : 70.60 % 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: 2.05 (0.19), residues: 2198 helix: 2.34 (0.14), residues: 1512 sheet: 0.40 (0.49), residues: 126 loop : -1.24 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 29 TYR 0.030 0.001 TYR E 232 PHE 0.011 0.001 PHE D 12 TRP 0.007 0.001 TRP E 74 HIS 0.003 0.001 HIS G 106 Details of bonding type rmsd covalent geometry : bond 0.00317 (18718) covalent geometry : angle 0.63968 (25445) SS BOND : bond 0.00221 ( 14) SS BOND : angle 1.50709 ( 28) hydrogen bonds : bond 0.03519 ( 1142) hydrogen bonds : angle 3.78982 ( 3363) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 237 time to evaluate : 0.722 Fit side-chains REVERT: A 14 ASP cc_start: 0.8624 (m-30) cc_final: 0.7625 (p0) REVERT: A 124 ASN cc_start: 0.8298 (OUTLIER) cc_final: 0.8013 (p0) REVERT: A 144 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8134 (mp0) REVERT: A 152 ARG cc_start: 0.6268 (ptm-80) cc_final: 0.5771 (mtm110) REVERT: A 240 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.7481 (m-80) REVERT: A 280 TYR cc_start: 0.8427 (t80) cc_final: 0.7726 (m-80) REVERT: A 306 ASN cc_start: 0.7605 (t0) cc_final: 0.7327 (t0) REVERT: A 317 PHE cc_start: 0.7894 (t80) cc_final: 0.7682 (m-80) REVERT: A 358 ASN cc_start: 0.8907 (t0) cc_final: 0.8569 (t0) REVERT: B 14 ASP cc_start: 0.8581 (m-30) cc_final: 0.7877 (p0) REVERT: B 124 ASN cc_start: 0.8494 (OUTLIER) cc_final: 0.8196 (p0) REVERT: B 144 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8120 (mp0) REVERT: B 152 ARG cc_start: 0.6331 (ptm-80) cc_final: 0.5839 (mtm110) REVERT: B 240 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.7550 (m-80) REVERT: B 266 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8275 (tt0) REVERT: B 306 ASN cc_start: 0.7618 (t0) cc_final: 0.7320 (t0) REVERT: B 317 PHE cc_start: 0.7757 (t80) cc_final: 0.7330 (m-80) REVERT: B 358 ASN cc_start: 0.8882 (t0) cc_final: 0.8522 (t0) REVERT: C 14 ASP cc_start: 0.8598 (m-30) cc_final: 0.7776 (p0) REVERT: C 90 GLN cc_start: 0.8259 (pp30) cc_final: 0.8042 (pp30) REVERT: C 124 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.7948 (p0) REVERT: C 144 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8093 (mp0) REVERT: C 152 ARG cc_start: 0.6143 (ptm-80) cc_final: 0.5654 (mtm110) REVERT: C 306 ASN cc_start: 0.7613 (t0) cc_final: 0.7370 (t0) REVERT: D 14 ASP cc_start: 0.8478 (m-30) cc_final: 0.7657 (p0) REVERT: D 152 ARG cc_start: 0.6274 (ptm-80) cc_final: 0.5787 (mtm110) REVERT: D 200 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8443 (mm-40) REVERT: D 306 ASN cc_start: 0.7707 (t0) cc_final: 0.7400 (t0) REVERT: D 317 PHE cc_start: 0.7922 (OUTLIER) cc_final: 0.7543 (m-80) REVERT: E 14 ASP cc_start: 0.8547 (m-30) cc_final: 0.7832 (p0) REVERT: E 144 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8167 (mp0) REVERT: E 152 ARG cc_start: 0.6311 (ptm-80) cc_final: 0.5863 (mtm110) REVERT: E 200 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8467 (mm-40) REVERT: E 203 LYS cc_start: 0.9233 (mmmt) cc_final: 0.8904 (mptt) REVERT: E 297 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7644 (pmm) REVERT: E 306 ASN cc_start: 0.7620 (t0) cc_final: 0.7290 (t0) REVERT: F 14 ASP cc_start: 0.8642 (m-30) cc_final: 0.8027 (t0) REVERT: F 124 ASN cc_start: 0.8253 (OUTLIER) cc_final: 0.7882 (p0) REVERT: F 144 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8374 (mp0) REVERT: F 203 LYS cc_start: 0.9234 (mmmt) cc_final: 0.8885 (mptt) REVERT: F 266 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8362 (tt0) REVERT: F 280 TYR cc_start: 0.8337 (t80) cc_final: 0.7725 (m-80) REVERT: F 358 ASN cc_start: 0.9055 (t0) cc_final: 0.8763 (t0) REVERT: G 14 ASP cc_start: 0.8623 (m-30) cc_final: 0.7827 (p0) REVERT: G 144 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8043 (mp0) REVERT: G 152 ARG cc_start: 0.6322 (ptm-80) cc_final: 0.5798 (mtm110) REVERT: G 200 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8484 (mm-40) REVERT: G 203 LYS cc_start: 0.9227 (mmmt) cc_final: 0.8821 (mmtt) REVERT: G 266 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8412 (tt0) REVERT: G 276 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7960 (mtm-85) REVERT: G 306 ASN cc_start: 0.7623 (t0) cc_final: 0.7381 (t0) outliers start: 96 outliers final: 55 residues processed: 311 average time/residue: 0.5466 time to fit residues: 192.1710 Evaluate side-chains 309 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 237 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 124 ASN Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 276 ARG Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 317 PHE Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 124 ASN Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 124 ASN Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 266 GLN Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 266 GLN Chi-restraints excluded: chain G residue 276 ARG Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 352 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 92 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 165 optimal weight: 0.0870 chunk 65 optimal weight: 1.9990 chunk 195 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 209 optimal weight: 2.9990 chunk 212 optimal weight: 6.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 355 ASN C 266 GLN C 355 ASN D 355 ASN E 355 ASN F 340 ASN F 355 ASN G 355 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.126584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.084930 restraints weight = 30394.391| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.45 r_work: 0.2970 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18732 Z= 0.122 Angle : 0.645 12.012 25473 Z= 0.305 Chirality : 0.039 0.196 3045 Planarity : 0.003 0.030 3052 Dihedral : 3.842 56.875 2426 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 4.24 % Allowed : 25.06 % Favored : 70.70 % 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: 2.15 (0.19), residues: 2198 helix: 2.41 (0.14), residues: 1512 sheet: 0.49 (0.49), residues: 126 loop : -1.19 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 29 TYR 0.030 0.001 TYR F 232 PHE 0.011 0.001 PHE D 12 TRP 0.007 0.001 TRP E 74 HIS 0.002 0.001 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00280 (18718) covalent geometry : angle 0.64330 (25445) SS BOND : bond 0.00245 ( 14) SS BOND : angle 1.44597 ( 28) hydrogen bonds : bond 0.03336 ( 1142) hydrogen bonds : angle 3.75240 ( 3363) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 242 time to evaluate : 0.505 Fit side-chains REVERT: A 14 ASP cc_start: 0.8610 (m-30) cc_final: 0.7620 (p0) REVERT: A 124 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.7997 (p0) REVERT: A 144 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8144 (mp0) REVERT: A 152 ARG cc_start: 0.6246 (ptm-80) cc_final: 0.5743 (mtm110) REVERT: A 240 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.7300 (m-80) REVERT: A 280 TYR cc_start: 0.8424 (t80) cc_final: 0.7730 (m-80) REVERT: A 306 ASN cc_start: 0.7594 (t0) cc_final: 0.7295 (t0) REVERT: A 358 ASN cc_start: 0.8917 (t0) cc_final: 0.8568 (t0) REVERT: A 368 TYR cc_start: 0.7748 (m-10) cc_final: 0.7531 (m-10) REVERT: B 14 ASP cc_start: 0.8582 (m-30) cc_final: 0.7922 (p0) REVERT: B 124 ASN cc_start: 0.8467 (OUTLIER) cc_final: 0.8165 (p0) REVERT: B 144 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8169 (mp0) REVERT: B 152 ARG cc_start: 0.6289 (ptm-80) cc_final: 0.5792 (mtm110) REVERT: B 240 PHE cc_start: 0.7741 (OUTLIER) cc_final: 0.7472 (m-80) REVERT: B 266 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8266 (tt0) REVERT: B 306 ASN cc_start: 0.7630 (t0) cc_final: 0.7361 (t0) REVERT: B 317 PHE cc_start: 0.7768 (t80) cc_final: 0.7367 (m-80) REVERT: B 358 ASN cc_start: 0.8926 (t0) cc_final: 0.8546 (t0) REVERT: C 14 ASP cc_start: 0.8582 (m-30) cc_final: 0.7804 (p0) REVERT: C 124 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.7971 (p0) REVERT: C 144 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8065 (mp0) REVERT: C 152 ARG cc_start: 0.6131 (ptm-80) cc_final: 0.5635 (mtm110) REVERT: C 200 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8349 (mm-40) REVERT: C 306 ASN cc_start: 0.7604 (t0) cc_final: 0.7372 (t0) REVERT: D 14 ASP cc_start: 0.8475 (m-30) cc_final: 0.7653 (p0) REVERT: D 152 ARG cc_start: 0.6260 (ptm-80) cc_final: 0.5765 (mtm110) REVERT: D 200 GLN cc_start: 0.8691 (mm-40) cc_final: 0.8452 (mm-40) REVERT: D 306 ASN cc_start: 0.7715 (t0) cc_final: 0.7402 (t0) REVERT: D 317 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.7387 (m-80) REVERT: E 14 ASP cc_start: 0.8512 (m-30) cc_final: 0.7812 (p0) REVERT: E 90 GLN cc_start: 0.8112 (pp30) cc_final: 0.7910 (pp30) REVERT: E 144 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8102 (mp0) REVERT: E 152 ARG cc_start: 0.6294 (ptm-80) cc_final: 0.5846 (mtm110) REVERT: E 200 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8504 (mm-40) REVERT: E 203 LYS cc_start: 0.9214 (mmmt) cc_final: 0.8902 (mptt) REVERT: E 280 TYR cc_start: 0.8501 (t80) cc_final: 0.7967 (m-80) REVERT: E 306 ASN cc_start: 0.7606 (t0) cc_final: 0.7288 (t0) REVERT: F 14 ASP cc_start: 0.8635 (m-30) cc_final: 0.8012 (t0) REVERT: F 124 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.7885 (p0) REVERT: F 144 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8416 (mp0) REVERT: F 203 LYS cc_start: 0.9224 (mmmt) cc_final: 0.8880 (mptt) REVERT: F 266 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8373 (tt0) REVERT: F 280 TYR cc_start: 0.8330 (t80) cc_final: 0.7708 (m-80) REVERT: F 358 ASN cc_start: 0.9058 (t0) cc_final: 0.8769 (t0) REVERT: G 14 ASP cc_start: 0.8588 (m-30) cc_final: 0.7792 (p0) REVERT: G 144 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8060 (mp0) REVERT: G 152 ARG cc_start: 0.6265 (ptm-80) cc_final: 0.5777 (mtm110) REVERT: G 200 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8466 (mm-40) REVERT: G 203 LYS cc_start: 0.9227 (mmmt) cc_final: 0.8805 (mmtt) REVERT: G 266 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8428 (tt0) REVERT: G 306 ASN cc_start: 0.7601 (t0) cc_final: 0.7371 (t0) outliers start: 87 outliers final: 56 residues processed: 306 average time/residue: 0.5545 time to fit residues: 191.7209 Evaluate side-chains 309 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 238 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 124 ASN Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 276 ARG Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 317 PHE Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 124 ASN Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 124 ASN Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 266 GLN Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 266 GLN Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 352 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 202 optimal weight: 0.0050 chunk 105 optimal weight: 0.9990 chunk 160 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 211 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 129 optimal weight: 8.9990 chunk 218 optimal weight: 0.3980 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 355 ASN C 266 GLN C 355 ASN D 355 ASN E 355 ASN F 340 ASN G 56 GLN G 355 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.126958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.085420 restraints weight = 30345.380| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.45 r_work: 0.2983 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18732 Z= 0.120 Angle : 0.658 11.522 25473 Z= 0.311 Chirality : 0.040 0.205 3045 Planarity : 0.003 0.035 3052 Dihedral : 3.856 58.159 2426 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.66 % Allowed : 25.69 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.19), residues: 2198 helix: 2.43 (0.14), residues: 1512 sheet: 0.47 (0.49), residues: 126 loop : -1.14 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 29 TYR 0.030 0.001 TYR G 232 PHE 0.010 0.001 PHE D 12 TRP 0.006 0.001 TRP E 74 HIS 0.002 0.000 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00271 (18718) covalent geometry : angle 0.65681 (25445) SS BOND : bond 0.00263 ( 14) SS BOND : angle 1.45157 ( 28) hydrogen bonds : bond 0.03254 ( 1142) hydrogen bonds : angle 3.75980 ( 3363) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 246 time to evaluate : 0.756 Fit side-chains REVERT: A 14 ASP cc_start: 0.8591 (m-30) cc_final: 0.7582 (p0) REVERT: A 124 ASN cc_start: 0.8259 (OUTLIER) cc_final: 0.7980 (p0) REVERT: A 144 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8118 (mp0) REVERT: A 152 ARG cc_start: 0.6240 (ptm-80) cc_final: 0.5704 (mtm110) REVERT: A 240 PHE cc_start: 0.7754 (OUTLIER) cc_final: 0.7176 (m-80) REVERT: A 280 TYR cc_start: 0.8430 (t80) cc_final: 0.7740 (m-80) REVERT: A 306 ASN cc_start: 0.7598 (t0) cc_final: 0.7309 (t0) REVERT: A 358 ASN cc_start: 0.8922 (t0) cc_final: 0.8569 (t0) REVERT: A 367 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.8031 (pm20) REVERT: B 14 ASP cc_start: 0.8707 (m-30) cc_final: 0.7941 (p0) REVERT: B 124 ASN cc_start: 0.8462 (OUTLIER) cc_final: 0.8150 (p0) REVERT: B 144 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8156 (mp0) REVERT: B 152 ARG cc_start: 0.6301 (ptm-80) cc_final: 0.5764 (mtm110) REVERT: B 240 PHE cc_start: 0.7750 (OUTLIER) cc_final: 0.7481 (m-80) REVERT: B 266 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8258 (tt0) REVERT: B 306 ASN cc_start: 0.7635 (t0) cc_final: 0.7356 (t0) REVERT: B 317 PHE cc_start: 0.7764 (t80) cc_final: 0.7369 (m-80) REVERT: B 358 ASN cc_start: 0.8936 (t0) cc_final: 0.8561 (t0) REVERT: C 14 ASP cc_start: 0.8571 (m-30) cc_final: 0.7681 (p0) REVERT: C 124 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.8030 (p0) REVERT: C 144 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: C 152 ARG cc_start: 0.6142 (ptm-80) cc_final: 0.5689 (mtm110) REVERT: C 306 ASN cc_start: 0.7607 (t0) cc_final: 0.7372 (t0) REVERT: D 14 ASP cc_start: 0.8480 (m-30) cc_final: 0.7664 (p0) REVERT: D 152 ARG cc_start: 0.6272 (ptm-80) cc_final: 0.5773 (mtm110) REVERT: D 200 GLN cc_start: 0.8707 (mm-40) cc_final: 0.8479 (mm-40) REVERT: D 240 PHE cc_start: 0.7649 (OUTLIER) cc_final: 0.6488 (t80) REVERT: D 306 ASN cc_start: 0.7711 (t0) cc_final: 0.7411 (t0) REVERT: D 317 PHE cc_start: 0.7752 (OUTLIER) cc_final: 0.7388 (m-80) REVERT: E 14 ASP cc_start: 0.8508 (m-30) cc_final: 0.7812 (p0) REVERT: E 144 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8095 (mp0) REVERT: E 152 ARG cc_start: 0.6289 (ptm-80) cc_final: 0.5863 (mtm110) REVERT: E 200 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8496 (mm-40) REVERT: E 203 LYS cc_start: 0.9205 (mmmt) cc_final: 0.8893 (mptt) REVERT: E 280 TYR cc_start: 0.8549 (t80) cc_final: 0.7988 (m-80) REVERT: E 297 MET cc_start: 0.7779 (pmm) cc_final: 0.7534 (pmm) REVERT: E 306 ASN cc_start: 0.7591 (t0) cc_final: 0.7296 (t0) REVERT: F 14 ASP cc_start: 0.8633 (m-30) cc_final: 0.8000 (t0) REVERT: F 124 ASN cc_start: 0.8267 (OUTLIER) cc_final: 0.7909 (p0) REVERT: F 203 LYS cc_start: 0.9241 (mmmt) cc_final: 0.8896 (mptt) REVERT: F 266 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8368 (tt0) REVERT: F 280 TYR cc_start: 0.8314 (t80) cc_final: 0.7692 (m-80) REVERT: F 358 ASN cc_start: 0.9076 (t0) cc_final: 0.8802 (t0) REVERT: G 14 ASP cc_start: 0.8587 (m-30) cc_final: 0.7813 (p0) REVERT: G 144 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8056 (mp0) REVERT: G 152 ARG cc_start: 0.6185 (ptm-80) cc_final: 0.5676 (mtm110) REVERT: G 200 GLN cc_start: 0.8703 (mm-40) cc_final: 0.8453 (mm-40) REVERT: G 203 LYS cc_start: 0.9266 (mmmt) cc_final: 0.8835 (mmtt) REVERT: G 266 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8393 (tt0) REVERT: G 306 ASN cc_start: 0.7599 (t0) cc_final: 0.7354 (t0) outliers start: 75 outliers final: 53 residues processed: 306 average time/residue: 0.6103 time to fit residues: 210.4475 Evaluate side-chains 307 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 237 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 124 ASN Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 276 ARG Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 317 PHE Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 124 ASN Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 124 ASN Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 266 GLN Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 266 GLN Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 352 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 103 optimal weight: 5.9990 chunk 126 optimal weight: 20.0000 chunk 77 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 222 optimal weight: 20.0000 chunk 217 optimal weight: 0.9980 chunk 220 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 177 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 56 GLN B 355 ASN C 266 GLN C 355 ASN D 355 ASN E 355 ASN F 340 ASN G 56 GLN G 355 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.125497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.083522 restraints weight = 30606.533| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.46 r_work: 0.2943 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18732 Z= 0.148 Angle : 0.681 12.557 25473 Z= 0.322 Chirality : 0.041 0.211 3045 Planarity : 0.003 0.033 3052 Dihedral : 3.857 56.574 2426 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.95 % Allowed : 25.55 % Favored : 70.50 % 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: 2.10 (0.19), residues: 2198 helix: 2.34 (0.14), residues: 1519 sheet: 0.46 (0.49), residues: 126 loop : -1.17 (0.29), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 29 TYR 0.032 0.001 TYR E 232 PHE 0.010 0.001 PHE D 12 TRP 0.010 0.001 TRP G 127 HIS 0.003 0.001 HIS C 106 Details of bonding type rmsd covalent geometry : bond 0.00355 (18718) covalent geometry : angle 0.67934 (25445) SS BOND : bond 0.00213 ( 14) SS BOND : angle 1.52083 ( 28) hydrogen bonds : bond 0.03520 ( 1142) hydrogen bonds : angle 3.84270 ( 3363) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6637.88 seconds wall clock time: 113 minutes 46.86 seconds (6826.86 seconds total)