Starting phenix.real_space_refine on Mon Jun 16 01:17:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bz8_45056/06_2025/9bz8_45056.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bz8_45056/06_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_45056/06_2025/9bz8_45056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bz8_45056/06_2025/9bz8_45056.map" model { file = "/net/cci-nas-00/data/ceres_data/9bz8_45056/06_2025/9bz8_45056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bz8_45056/06_2025/9bz8_45056.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D, G, F Time building chain proxies: 5.85, per 1000 atoms: 0.32 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 C 66 " - pdb=" SG CYS C 267 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 267 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 267 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 267 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 267 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 267 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 248 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 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: 4.04 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.49 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: 4.85 Time building geometry restraints manager: 4.86 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } 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: 0.470 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: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 32.790 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 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:11.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.090 ------------------------------------------------------------------------------- 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 : 7.04 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP A 74 HIS 0.001 0.000 HIS C 106 PHE 0.008 0.001 PHE B 12 TYR 0.006 0.001 TYR A 232 ARG 0.007 0.001 ARG C 29 Details of bonding type rmsd hydrogen bonds : bond 0.09457 ( 1142) hydrogen bonds : angle 4.15936 ( 3363) SS BOND : bond 0.00115 ( 14) SS BOND : angle 4.56803 ( 28) covalent geometry : bond 0.00218 (18718) covalent geometry : angle 0.51221 (25445) *********************** 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 : 1.851 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: 0.7777 (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: 0.6233 (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: 1.3653 time to fit residues: 631.3233 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 : 1.888 ------------------------------------------------------------------------------- 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 189 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 203 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.124247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.082278 restraints weight = 30893.060| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.42 r_work: 0.2910 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 18732 Z= 0.247 Angle : 0.666 8.376 25473 Z= 0.327 Chirality : 0.042 0.221 3045 Planarity : 0.004 0.030 3052 Dihedral : 4.565 48.918 2451 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 6.83 % Allowed : 23.21 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.19), residues: 2198 helix: 2.29 (0.13), residues: 1526 sheet: -0.10 (0.47), residues: 126 loop : -1.42 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 85 HIS 0.005 0.001 HIS B 106 PHE 0.017 0.002 PHE B 333 TYR 0.025 0.002 TYR A 232 ARG 0.006 0.001 ARG B 128 Details of bonding type rmsd hydrogen bonds : bond 0.04323 ( 1142) hydrogen bonds : angle 3.96256 ( 3363) SS BOND : bond 0.00198 ( 14) SS BOND : angle 2.09238 ( 28) covalent geometry : bond 0.00600 (18718) covalent geometry : angle 0.66281 (25445) *********************** 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 391 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 251 time to evaluate : 2.095 Fit side-chains revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8617 (m-30) cc_final: 0.8006 (t0) REVERT: A 124 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.7986 (p0) REVERT: A 144 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8186 (mp0) REVERT: A 152 ARG cc_start: 0.6272 (ptm-80) cc_final: 0.5855 (mtm110) REVERT: A 240 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.7207 (m-80) REVERT: A 297 MET cc_start: 0.7820 (ptp) cc_final: 0.7597 (pmm) REVERT: A 358 ASN cc_start: 0.8805 (t0) cc_final: 0.8474 (t0) REVERT: B 14 ASP cc_start: 0.8788 (m-30) cc_final: 0.7891 (p0) REVERT: B 124 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.8181 (p0) REVERT: B 144 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8222 (mp0) REVERT: B 152 ARG cc_start: 0.6220 (ptm-80) cc_final: 0.5769 (mtm110) REVERT: B 240 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.7365 (m-80) REVERT: B 306 ASN cc_start: 0.7449 (t0) cc_final: 0.7239 (t0) REVERT: B 317 PHE cc_start: 0.7784 (t80) cc_final: 0.7358 (m-80) REVERT: B 358 ASN cc_start: 0.8832 (t0) cc_final: 0.8455 (t0) REVERT: C 14 ASP cc_start: 0.8719 (m-30) cc_final: 0.7880 (p0) REVERT: C 124 ASN cc_start: 0.8377 (OUTLIER) cc_final: 0.8075 (p0) REVERT: C 152 ARG cc_start: 0.6099 (ptm-80) cc_final: 0.5744 (mtm110) REVERT: C 297 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7699 (pmm) REVERT: C 327 TYR cc_start: 0.6202 (t80) cc_final: 0.6001 (m-10) REVERT: D 14 ASP cc_start: 0.8499 (m-30) cc_final: 0.7660 (p0) REVERT: D 124 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.8035 (p0) REVERT: D 152 ARG cc_start: 0.6243 (ptm-80) cc_final: 0.5803 (mtm110) REVERT: D 306 ASN cc_start: 0.7702 (t0) cc_final: 0.7465 (t0) REVERT: E 14 ASP cc_start: 0.8694 (m-30) cc_final: 0.7858 (p0) REVERT: E 144 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: E 152 ARG cc_start: 0.6183 (ptm-80) cc_final: 0.5755 (mtm110) REVERT: E 200 GLN cc_start: 0.8898 (mm-40) cc_final: 0.8317 (mm-40) REVERT: E 297 MET cc_start: 0.7990 (pmm) cc_final: 0.7702 (pmm) REVERT: E 306 ASN cc_start: 0.7586 (t0) cc_final: 0.7288 (t0) REVERT: F 14 ASP cc_start: 0.8637 (m-30) cc_final: 0.7866 (t0) REVERT: F 152 ARG cc_start: 0.6271 (ptm-80) cc_final: 0.5994 (mtp-110) REVERT: F 358 ASN cc_start: 0.8874 (t0) cc_final: 0.8609 (t0) REVERT: G 14 ASP cc_start: 0.8733 (m-30) cc_final: 0.7918 (p0) REVERT: G 144 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8041 (mp0) REVERT: G 152 ARG cc_start: 0.6158 (ptm-80) cc_final: 0.5675 (mtm110) REVERT: G 317 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7587 (m-80) REVERT: G 327 TYR cc_start: 0.6135 (t80) cc_final: 0.5858 (m-80) outliers start: 140 outliers final: 47 residues processed: 363 average time/residue: 1.3666 time to fit residues: 561.8376 Evaluate side-chains 302 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 243 time to evaluate : 2.171 ------------------------------------------------------------------------------- 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 313 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 352 VAL Chi-restraints excluded: chain C residue 16 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 255 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 34 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 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 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 287 VAL 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 287 VAL Chi-restraints excluded: chain F residue 352 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 287 VAL Chi-restraints excluded: chain G residue 317 PHE 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 35 optimal weight: 8.9990 chunk 55 optimal weight: 0.7980 chunk 110 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 210 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 355 ASN C 266 GLN C 355 ASN D 355 ASN E 340 ASN E 355 ASN F 355 ASN G 5 HIS G 56 GLN G 355 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.126061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.084114 restraints weight = 30678.379| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.44 r_work: 0.2951 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18732 Z= 0.135 Angle : 0.591 7.833 25473 Z= 0.284 Chirality : 0.039 0.178 3045 Planarity : 0.003 0.028 3052 Dihedral : 4.495 52.339 2444 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 5.56 % Allowed : 24.04 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.19), residues: 2198 helix: 2.44 (0.13), residues: 1519 sheet: -0.09 (0.47), residues: 126 loop : -1.36 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 85 HIS 0.003 0.001 HIS B 106 PHE 0.011 0.001 PHE E 83 TYR 0.023 0.001 TYR E 232 ARG 0.006 0.001 ARG F 29 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 1142) hydrogen bonds : angle 3.77288 ( 3363) SS BOND : bond 0.00125 ( 14) SS BOND : angle 1.69387 ( 28) covalent geometry : bond 0.00321 (18718) covalent geometry : angle 0.58819 (25445) *********************** 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 368 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 254 time to evaluate : 4.953 Fit side-chains revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8599 (m-30) cc_final: 0.8018 (t0) REVERT: A 124 ASN cc_start: 0.8240 (OUTLIER) cc_final: 0.7912 (p0) REVERT: A 144 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8128 (mp0) REVERT: A 152 ARG cc_start: 0.6327 (ptm-80) cc_final: 0.5833 (mtm110) REVERT: A 240 PHE cc_start: 0.7791 (OUTLIER) cc_final: 0.7254 (m-80) REVERT: A 306 ASN cc_start: 0.7471 (t0) cc_final: 0.7270 (t0) REVERT: A 358 ASN cc_start: 0.8816 (t0) cc_final: 0.8485 (t0) REVERT: B 14 ASP cc_start: 0.8729 (m-30) cc_final: 0.7865 (p0) REVERT: B 124 ASN cc_start: 0.8441 (OUTLIER) cc_final: 0.8142 (p0) REVERT: B 144 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8121 (mp0) REVERT: B 152 ARG cc_start: 0.6238 (ptm-80) cc_final: 0.5740 (mtm110) REVERT: B 240 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.7429 (m-80) REVERT: B 306 ASN cc_start: 0.7585 (t0) cc_final: 0.7105 (t0) REVERT: B 309 LYS cc_start: 0.9081 (mmtt) cc_final: 0.8881 (mmtp) REVERT: B 358 ASN cc_start: 0.8835 (t0) cc_final: 0.8459 (t0) REVERT: C 124 ASN cc_start: 0.8350 (OUTLIER) cc_final: 0.8059 (p0) REVERT: C 152 ARG cc_start: 0.6157 (ptm-80) cc_final: 0.5717 (mtm110) REVERT: C 297 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7606 (pmm) REVERT: D 14 ASP cc_start: 0.8445 (m-30) cc_final: 0.7627 (p0) REVERT: D 124 ASN cc_start: 0.8327 (OUTLIER) cc_final: 0.8064 (p0) REVERT: D 152 ARG cc_start: 0.6243 (ptm-80) cc_final: 0.5735 (mtm110) REVERT: D 306 ASN cc_start: 0.7599 (t0) cc_final: 0.7309 (t0) REVERT: E 14 ASP cc_start: 0.8648 (m-30) cc_final: 0.7813 (p0) REVERT: E 144 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8038 (mp0) REVERT: E 152 ARG cc_start: 0.6300 (ptm-80) cc_final: 0.5839 (mtm110) REVERT: E 203 LYS cc_start: 0.9280 (mmmt) cc_final: 0.8840 (mmtt) REVERT: E 297 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7772 (pmm) REVERT: E 306 ASN cc_start: 0.7596 (t0) cc_final: 0.7185 (t0) REVERT: F 9 GLU cc_start: 0.8680 (tt0) cc_final: 0.8381 (tt0) REVERT: F 14 ASP cc_start: 0.8642 (m-30) cc_final: 0.7857 (t0) REVERT: F 124 ASN cc_start: 0.8246 (OUTLIER) cc_final: 0.7943 (p0) REVERT: F 144 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8287 (mp0) REVERT: F 152 ARG cc_start: 0.6245 (ptm-80) cc_final: 0.5845 (mtm110) REVERT: F 266 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8250 (tt0) REVERT: F 338 GLU cc_start: 0.8997 (tt0) cc_final: 0.8467 (tp30) REVERT: F 340 ASN cc_start: 0.9045 (OUTLIER) cc_final: 0.8806 (t0) REVERT: F 354 GLU cc_start: 0.9071 (tp30) cc_final: 0.8688 (tp30) REVERT: F 358 ASN cc_start: 0.8881 (t0) cc_final: 0.8638 (t0) REVERT: G 14 ASP cc_start: 0.8653 (m-30) cc_final: 0.7760 (p0) REVERT: G 128 ARG cc_start: 0.8731 (tmm-80) cc_final: 0.8473 (ttt-90) REVERT: G 144 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: G 152 ARG cc_start: 0.6261 (ptm-80) cc_final: 0.5720 (mtm110) REVERT: G 327 TYR cc_start: 0.6116 (t80) cc_final: 0.5837 (m-10) outliers start: 114 outliers final: 45 residues processed: 343 average time/residue: 1.4833 time to fit residues: 590.4038 Evaluate side-chains 296 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 236 time to evaluate : 1.998 ------------------------------------------------------------------------------- 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 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 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 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 297 MET Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 34 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 272 VAL Chi-restraints excluded: chain D residue 276 ARG Chi-restraints excluded: chain D residue 290 MET 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 240 PHE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 255 LEU 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 340 ASN 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 352 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 163 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 133 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 340 ASN C 355 ASN ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 ASN D 355 ASN E 355 ASN F 355 ASN G 56 GLN G 355 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.125646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.084055 restraints weight = 30660.499| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.43 r_work: 0.2947 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18732 Z= 0.140 Angle : 0.606 9.049 25473 Z= 0.288 Chirality : 0.040 0.178 3045 Planarity : 0.003 0.030 3052 Dihedral : 4.544 53.204 2443 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 5.46 % Allowed : 23.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.19), residues: 2198 helix: 2.42 (0.13), residues: 1512 sheet: 0.06 (0.48), residues: 126 loop : -1.31 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 85 HIS 0.003 0.001 HIS B 106 PHE 0.010 0.001 PHE D 12 TYR 0.026 0.001 TYR E 232 ARG 0.006 0.001 ARG D 29 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 1142) hydrogen bonds : angle 3.75942 ( 3363) SS BOND : bond 0.00140 ( 14) SS BOND : angle 1.58634 ( 28) covalent geometry : bond 0.00334 (18718) covalent geometry : angle 0.60388 (25445) *********************** 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 355 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 243 time to evaluate : 2.161 Fit side-chains revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8504 (m-30) cc_final: 0.8014 (t0) REVERT: A 124 ASN cc_start: 0.8149 (OUTLIER) cc_final: 0.7766 (p0) REVERT: A 144 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.8013 (mp0) REVERT: A 152 ARG cc_start: 0.6286 (ptm-80) cc_final: 0.5789 (mtm110) REVERT: A 240 PHE cc_start: 0.7690 (OUTLIER) cc_final: 0.7148 (m-80) REVERT: A 306 ASN cc_start: 0.7469 (t0) cc_final: 0.7226 (t0) REVERT: A 358 ASN cc_start: 0.8814 (t0) cc_final: 0.8473 (t0) REVERT: B 14 ASP cc_start: 0.8576 (m-30) cc_final: 0.7811 (p0) REVERT: B 124 ASN cc_start: 0.8350 (OUTLIER) cc_final: 0.8004 (p0) REVERT: B 144 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8001 (mp0) REVERT: B 152 ARG cc_start: 0.6165 (ptm-80) cc_final: 0.5720 (mtm110) REVERT: B 203 LYS cc_start: 0.9196 (mmmt) cc_final: 0.8772 (mmtt) REVERT: B 240 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.7343 (m-80) REVERT: B 306 ASN cc_start: 0.7564 (t0) cc_final: 0.7129 (t0) REVERT: B 317 PHE cc_start: 0.7758 (t80) cc_final: 0.7350 (m-80) REVERT: B 358 ASN cc_start: 0.8851 (t0) cc_final: 0.8455 (t0) REVERT: C 14 ASP cc_start: 0.8480 (m-30) cc_final: 0.7695 (p0) REVERT: C 124 ASN cc_start: 0.8254 (OUTLIER) cc_final: 0.7958 (p0) REVERT: C 152 ARG cc_start: 0.6117 (ptm-80) cc_final: 0.5692 (mtm110) REVERT: C 306 ASN cc_start: 0.7367 (t0) cc_final: 0.7117 (t0) REVERT: C 352 VAL cc_start: 0.8730 (OUTLIER) cc_final: 0.8507 (t) REVERT: D 14 ASP cc_start: 0.8288 (m-30) cc_final: 0.7575 (p0) REVERT: D 124 ASN cc_start: 0.8297 (OUTLIER) cc_final: 0.8004 (p0) REVERT: D 152 ARG cc_start: 0.6205 (ptm-80) cc_final: 0.5731 (mtm110) REVERT: D 240 PHE cc_start: 0.7690 (OUTLIER) cc_final: 0.6379 (t80) REVERT: D 306 ASN cc_start: 0.7583 (t0) cc_final: 0.7304 (t0) REVERT: E 14 ASP cc_start: 0.8501 (m-30) cc_final: 0.7780 (p0) REVERT: E 144 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: E 152 ARG cc_start: 0.6223 (ptm-80) cc_final: 0.5785 (mtm110) REVERT: E 203 LYS cc_start: 0.9310 (mmmt) cc_final: 0.8868 (mmtt) REVERT: E 297 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7680 (pmm) REVERT: E 306 ASN cc_start: 0.7565 (t0) cc_final: 0.7324 (t0) REVERT: F 14 ASP cc_start: 0.8574 (m-30) cc_final: 0.7845 (t0) REVERT: F 124 ASN cc_start: 0.8134 (OUTLIER) cc_final: 0.7791 (p0) REVERT: F 152 ARG cc_start: 0.6188 (ptm-80) cc_final: 0.5813 (mtm110) REVERT: F 203 LYS cc_start: 0.9201 (mmmt) cc_final: 0.8851 (mptt) REVERT: F 266 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8136 (tt0) REVERT: F 358 ASN cc_start: 0.8903 (t0) cc_final: 0.8633 (t0) REVERT: G 14 ASP cc_start: 0.8479 (m-30) cc_final: 0.7703 (p0) REVERT: G 128 ARG cc_start: 0.8651 (tmm-80) cc_final: 0.8372 (ttt-90) REVERT: G 144 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: G 152 ARG cc_start: 0.6231 (ptm-80) cc_final: 0.5711 (mtm110) REVERT: G 203 LYS cc_start: 0.9265 (mmmt) cc_final: 0.8852 (mmtt) REVERT: G 317 PHE cc_start: 0.7895 (t80) cc_final: 0.7577 (m-80) outliers start: 112 outliers final: 53 residues processed: 330 average time/residue: 1.3663 time to fit residues: 520.0538 Evaluate side-chains 304 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 236 time to evaluate : 3.163 ------------------------------------------------------------------------------- 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 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 352 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 90 GLN 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 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 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 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 90 GLN 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 255 LEU Chi-restraints excluded: chain F residue 266 GLN Chi-restraints excluded: chain F residue 287 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 255 LEU 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 56 optimal weight: 1.9990 chunk 194 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 184 optimal weight: 0.9980 chunk 218 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 174 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 chunk 155 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 340 ASN C 355 ASN D 355 ASN E 340 ASN E 355 ASN F 282 ASN F 340 ASN F 355 ASN G 56 GLN G 282 ASN G 355 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.125840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.083892 restraints weight = 30654.072| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.46 r_work: 0.2947 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18732 Z= 0.135 Angle : 0.607 9.042 25473 Z= 0.288 Chirality : 0.040 0.183 3045 Planarity : 0.003 0.029 3052 Dihedral : 4.413 53.945 2440 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 5.70 % Allowed : 23.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.19), residues: 2198 helix: 2.41 (0.13), residues: 1519 sheet: 0.16 (0.48), residues: 126 loop : -1.22 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 85 HIS 0.003 0.001 HIS F 106 PHE 0.010 0.001 PHE D 12 TYR 0.026 0.001 TYR E 232 ARG 0.006 0.001 ARG F 29 Details of bonding type rmsd hydrogen bonds : bond 0.03496 ( 1142) hydrogen bonds : angle 3.72354 ( 3363) SS BOND : bond 0.00161 ( 14) SS BOND : angle 1.49631 ( 28) covalent geometry : bond 0.00323 (18718) covalent geometry : angle 0.60494 (25445) *********************** 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: 117 poor density : 245 time to evaluate : 2.564 Fit side-chains REVERT: A 14 ASP cc_start: 0.8489 (m-30) cc_final: 0.7612 (p0) REVERT: A 124 ASN cc_start: 0.8158 (OUTLIER) cc_final: 0.7751 (p0) REVERT: A 144 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7997 (mp0) REVERT: A 152 ARG cc_start: 0.6288 (ptm-80) cc_final: 0.5792 (mtm110) REVERT: A 240 PHE cc_start: 0.7684 (OUTLIER) cc_final: 0.7161 (m-80) REVERT: A 306 ASN cc_start: 0.7528 (t0) cc_final: 0.7288 (t0) REVERT: A 358 ASN cc_start: 0.8819 (t0) cc_final: 0.8470 (t0) REVERT: B 14 ASP cc_start: 0.8553 (m-30) cc_final: 0.7804 (p0) REVERT: B 124 ASN cc_start: 0.8324 (OUTLIER) cc_final: 0.7901 (p0) REVERT: B 144 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7964 (mp0) REVERT: B 152 ARG cc_start: 0.6235 (ptm-80) cc_final: 0.5787 (mtm110) REVERT: B 203 LYS cc_start: 0.9191 (mmmt) cc_final: 0.8772 (mmtt) REVERT: B 240 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.7418 (m-80) REVERT: B 266 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8149 (tt0) REVERT: B 358 ASN cc_start: 0.8869 (t0) cc_final: 0.8473 (t0) REVERT: C 14 ASP cc_start: 0.8477 (m-30) cc_final: 0.7704 (p0) REVERT: C 124 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.7933 (p0) REVERT: C 144 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7982 (mp0) REVERT: C 152 ARG cc_start: 0.6054 (ptm-80) cc_final: 0.5618 (mtm110) REVERT: C 200 GLN cc_start: 0.8589 (mm-40) cc_final: 0.8378 (mm-40) REVERT: C 297 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7958 (pmt) REVERT: C 306 ASN cc_start: 0.7549 (t0) cc_final: 0.7278 (t0) REVERT: D 14 ASP cc_start: 0.8298 (m-30) cc_final: 0.7580 (p0) REVERT: D 124 ASN cc_start: 0.8322 (OUTLIER) cc_final: 0.7976 (p0) REVERT: D 152 ARG cc_start: 0.6213 (ptm-80) cc_final: 0.5725 (mtm110) REVERT: D 240 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.6382 (t80) REVERT: D 266 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8368 (tt0) REVERT: D 306 ASN cc_start: 0.7601 (t0) cc_final: 0.7295 (t0) REVERT: E 14 ASP cc_start: 0.8472 (m-30) cc_final: 0.7781 (p0) REVERT: E 144 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7908 (mp0) REVERT: E 152 ARG cc_start: 0.6227 (ptm-80) cc_final: 0.5752 (mtm110) REVERT: E 200 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8552 (mm-40) REVERT: E 203 LYS cc_start: 0.9273 (mmmt) cc_final: 0.8844 (mmtt) REVERT: E 266 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8138 (tt0) REVERT: E 306 ASN cc_start: 0.7576 (t0) cc_final: 0.7330 (t0) REVERT: F 14 ASP cc_start: 0.8560 (m-30) cc_final: 0.7847 (t0) REVERT: F 144 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8203 (mp0) REVERT: F 152 ARG cc_start: 0.6127 (ptm-80) cc_final: 0.5716 (mtm110) REVERT: F 203 LYS cc_start: 0.9218 (mmmt) cc_final: 0.8860 (mptt) REVERT: F 232 TYR cc_start: 0.7738 (t80) cc_final: 0.7402 (t80) REVERT: F 266 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8135 (tt0) REVERT: F 297 MET cc_start: 0.8017 (pmt) cc_final: 0.7776 (pmt) REVERT: F 358 ASN cc_start: 0.8952 (t0) cc_final: 0.8678 (t0) REVERT: G 14 ASP cc_start: 0.8459 (m-30) cc_final: 0.7706 (p0) REVERT: G 128 ARG cc_start: 0.8596 (tmm-80) cc_final: 0.8301 (ttt180) REVERT: G 144 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: G 152 ARG cc_start: 0.6246 (ptm-80) cc_final: 0.5714 (mtm110) REVERT: G 203 LYS cc_start: 0.9245 (mmmt) cc_final: 0.8844 (mmtt) REVERT: G 266 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8240 (tt0) REVERT: G 317 PHE cc_start: 0.7904 (t80) cc_final: 0.7594 (m-80) outliers start: 117 outliers final: 57 residues processed: 340 average time/residue: 1.1008 time to fit residues: 428.0453 Evaluate side-chains 320 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 245 time to evaluate : 1.797 ------------------------------------------------------------------------------- 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 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 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 266 GLN Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 297 MET 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 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 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 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 224 ILE Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 266 GLN 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 255 LEU Chi-restraints excluded: chain F residue 266 GLN Chi-restraints excluded: chain F residue 287 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 163 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 198 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 210 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 340 ASN B 355 ASN C 340 ASN C 355 ASN D 355 ASN E 355 ASN F 282 ASN G 56 GLN G 355 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.126072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.084473 restraints weight = 30597.984| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.44 r_work: 0.2960 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18732 Z= 0.128 Angle : 0.607 8.093 25473 Z= 0.289 Chirality : 0.039 0.186 3045 Planarity : 0.003 0.028 3052 Dihedral : 4.415 54.293 2438 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 5.36 % Allowed : 23.55 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.19), residues: 2198 helix: 2.44 (0.14), residues: 1512 sheet: 0.22 (0.48), residues: 126 loop : -1.23 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 85 HIS 0.002 0.001 HIS A 106 PHE 0.010 0.001 PHE D 12 TYR 0.027 0.001 TYR G 327 ARG 0.007 0.001 ARG F 29 Details of bonding type rmsd hydrogen bonds : bond 0.03438 ( 1142) hydrogen bonds : angle 3.71097 ( 3363) SS BOND : bond 0.00189 ( 14) SS BOND : angle 1.51451 ( 28) covalent geometry : bond 0.00302 (18718) covalent geometry : angle 0.60551 (25445) *********************** 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 356 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 246 time to evaluate : 1.833 Fit side-chains REVERT: A 14 ASP cc_start: 0.8626 (m-30) cc_final: 0.7675 (p0) REVERT: A 124 ASN cc_start: 0.8315 (OUTLIER) cc_final: 0.7901 (p0) REVERT: A 144 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8105 (mp0) REVERT: A 152 ARG cc_start: 0.6332 (ptm-80) cc_final: 0.5827 (mtm110) REVERT: A 240 PHE cc_start: 0.7785 (OUTLIER) cc_final: 0.7263 (m-80) REVERT: A 306 ASN cc_start: 0.7576 (t0) cc_final: 0.7325 (t0) REVERT: A 358 ASN cc_start: 0.8827 (t0) cc_final: 0.8469 (t0) REVERT: B 14 ASP cc_start: 0.8634 (m-30) cc_final: 0.7847 (p0) REVERT: B 144 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8080 (mp0) REVERT: B 152 ARG cc_start: 0.6305 (ptm-80) cc_final: 0.5799 (mtm110) REVERT: B 203 LYS cc_start: 0.9154 (mmmt) cc_final: 0.8736 (mmtt) REVERT: B 240 PHE cc_start: 0.7750 (OUTLIER) cc_final: 0.7489 (m-80) REVERT: B 306 ASN cc_start: 0.7501 (t0) cc_final: 0.7263 (t0) REVERT: B 317 PHE cc_start: 0.7805 (t80) cc_final: 0.7442 (m-80) REVERT: B 358 ASN cc_start: 0.8858 (t0) cc_final: 0.8479 (t0) REVERT: C 14 ASP cc_start: 0.8577 (m-30) cc_final: 0.7747 (p0) REVERT: C 124 ASN cc_start: 0.8379 (OUTLIER) cc_final: 0.7981 (p0) REVERT: C 144 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8081 (mp0) REVERT: C 152 ARG cc_start: 0.6108 (ptm-80) cc_final: 0.5657 (mtm110) REVERT: C 297 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8070 (pmt) REVERT: C 306 ASN cc_start: 0.7627 (t0) cc_final: 0.7351 (t0) REVERT: D 14 ASP cc_start: 0.8442 (m-30) cc_final: 0.7633 (p0) REVERT: D 124 ASN cc_start: 0.8310 (OUTLIER) cc_final: 0.7898 (p0) REVERT: D 152 ARG cc_start: 0.6378 (ptm-80) cc_final: 0.5866 (mtm110) REVERT: D 240 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.6548 (t80) REVERT: D 266 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8466 (tt0) REVERT: D 306 ASN cc_start: 0.7659 (t0) cc_final: 0.7359 (t0) REVERT: E 14 ASP cc_start: 0.8581 (m-30) cc_final: 0.7854 (p0) REVERT: E 144 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: E 152 ARG cc_start: 0.6254 (ptm-80) cc_final: 0.5753 (mtm110) REVERT: E 203 LYS cc_start: 0.9266 (mmmt) cc_final: 0.8918 (mptt) REVERT: E 266 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8212 (tt0) REVERT: E 306 ASN cc_start: 0.7597 (t0) cc_final: 0.7329 (t0) REVERT: F 14 ASP cc_start: 0.8667 (m-30) cc_final: 0.7857 (t0) REVERT: F 144 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8354 (mp0) REVERT: F 152 ARG cc_start: 0.6200 (ptm-80) cc_final: 0.5777 (mtm110) REVERT: F 203 LYS cc_start: 0.9216 (mmmt) cc_final: 0.8864 (mptt) REVERT: F 266 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8248 (tt0) REVERT: F 280 TYR cc_start: 0.8381 (t80) cc_final: 0.7715 (m-80) REVERT: F 358 ASN cc_start: 0.8971 (t0) cc_final: 0.8698 (t0) REVERT: G 14 ASP cc_start: 0.8576 (m-30) cc_final: 0.7762 (p0) REVERT: G 56 GLN cc_start: 0.8941 (mm-40) cc_final: 0.8734 (mm-40) REVERT: G 128 ARG cc_start: 0.8680 (tmm-80) cc_final: 0.8405 (ttt180) REVERT: G 144 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7942 (mp0) REVERT: G 152 ARG cc_start: 0.6238 (ptm-80) cc_final: 0.5718 (mtm110) REVERT: G 203 LYS cc_start: 0.9243 (mmmt) cc_final: 0.8890 (mmtt) REVERT: G 266 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8347 (tt0) REVERT: G 317 PHE cc_start: 0.7911 (t80) cc_final: 0.7596 (m-80) outliers start: 110 outliers final: 54 residues processed: 332 average time/residue: 1.1857 time to fit residues: 450.6881 Evaluate side-chains 308 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 238 time to evaluate : 2.076 ------------------------------------------------------------------------------- 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 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 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 337 LEU 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 297 MET Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 124 ASN 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 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 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 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 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 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 164 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 213 optimal weight: 0.1980 chunk 193 optimal weight: 0.0970 chunk 150 optimal weight: 4.9990 chunk 88 optimal weight: 0.5980 chunk 181 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 340 ASN C 355 ASN D 340 ASN D 355 ASN E 355 ASN F 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 = 0.3820 r_free = 0.3820 target = 0.127776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.086210 restraints weight = 30454.264| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.48 r_work: 0.2997 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18732 Z= 0.113 Angle : 0.613 10.847 25473 Z= 0.290 Chirality : 0.039 0.185 3045 Planarity : 0.003 0.030 3052 Dihedral : 4.498 55.699 2438 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.34 % Allowed : 24.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.19), residues: 2198 helix: 2.52 (0.14), residues: 1512 sheet: 0.20 (0.48), residues: 126 loop : -1.16 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 104 HIS 0.002 0.000 HIS F 106 PHE 0.010 0.001 PHE D 12 TYR 0.026 0.001 TYR F 232 ARG 0.007 0.001 ARG D 29 Details of bonding type rmsd hydrogen bonds : bond 0.03138 ( 1142) hydrogen bonds : angle 3.64387 ( 3363) SS BOND : bond 0.00250 ( 14) SS BOND : angle 1.40902 ( 28) covalent geometry : bond 0.00250 (18718) covalent geometry : angle 0.61150 (25445) *********************** 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 334 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 245 time to evaluate : 1.888 Fit side-chains REVERT: A 14 ASP cc_start: 0.8464 (m-30) cc_final: 0.7602 (p0) REVERT: A 124 ASN cc_start: 0.8289 (OUTLIER) cc_final: 0.7795 (p0) REVERT: A 144 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8016 (mp0) REVERT: A 152 ARG cc_start: 0.6282 (ptm-80) cc_final: 0.5776 (mtm110) REVERT: A 240 PHE cc_start: 0.7547 (OUTLIER) cc_final: 0.6919 (m-80) REVERT: A 306 ASN cc_start: 0.7553 (t0) cc_final: 0.7314 (t0) REVERT: A 358 ASN cc_start: 0.8817 (t0) cc_final: 0.8451 (t0) REVERT: B 14 ASP cc_start: 0.8515 (m-30) cc_final: 0.7806 (p0) REVERT: B 144 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: B 152 ARG cc_start: 0.6170 (ptm-80) cc_final: 0.5686 (mtm110) REVERT: B 203 LYS cc_start: 0.9132 (mmmt) cc_final: 0.8745 (mmtt) REVERT: B 240 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.7321 (m-80) REVERT: B 266 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8043 (tt0) REVERT: B 306 ASN cc_start: 0.7507 (t0) cc_final: 0.7267 (t0) REVERT: B 358 ASN cc_start: 0.8854 (t0) cc_final: 0.8484 (t0) REVERT: C 14 ASP cc_start: 0.8438 (m-30) cc_final: 0.7630 (p0) REVERT: C 144 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7965 (mp0) REVERT: C 152 ARG cc_start: 0.6083 (ptm-80) cc_final: 0.5634 (mtm110) REVERT: C 297 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7872 (pmt) REVERT: C 306 ASN cc_start: 0.7771 (t0) cc_final: 0.7512 (t0) REVERT: C 352 VAL cc_start: 0.8768 (OUTLIER) cc_final: 0.8541 (t) REVERT: D 14 ASP cc_start: 0.8277 (m-30) cc_final: 0.7584 (p0) REVERT: D 124 ASN cc_start: 0.8211 (OUTLIER) cc_final: 0.7694 (p0) REVERT: D 152 ARG cc_start: 0.6350 (ptm-80) cc_final: 0.5826 (mtm110) REVERT: D 240 PHE cc_start: 0.7643 (OUTLIER) cc_final: 0.6357 (t80) REVERT: D 306 ASN cc_start: 0.7631 (t0) cc_final: 0.7345 (t0) REVERT: E 14 ASP cc_start: 0.8441 (m-30) cc_final: 0.7764 (p0) REVERT: E 144 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7978 (mp0) REVERT: E 152 ARG cc_start: 0.6226 (ptm-80) cc_final: 0.5724 (mtm110) REVERT: E 203 LYS cc_start: 0.9213 (mmmt) cc_final: 0.8914 (mptt) REVERT: E 266 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8082 (tt0) REVERT: E 306 ASN cc_start: 0.7581 (t0) cc_final: 0.7308 (t0) REVERT: F 14 ASP cc_start: 0.8504 (m-30) cc_final: 0.7860 (t0) REVERT: F 144 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8240 (mp0) REVERT: F 152 ARG cc_start: 0.6176 (ptm-80) cc_final: 0.5751 (mtm110) REVERT: F 203 LYS cc_start: 0.9208 (mmmt) cc_final: 0.8869 (mptt) REVERT: F 266 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8104 (tt0) REVERT: F 280 TYR cc_start: 0.8116 (t80) cc_final: 0.7586 (m-80) REVERT: F 297 MET cc_start: 0.7915 (pmt) cc_final: 0.7653 (pmt) REVERT: F 358 ASN cc_start: 0.8976 (t0) cc_final: 0.8673 (t0) REVERT: G 14 ASP cc_start: 0.8409 (m-30) cc_final: 0.7722 (p0) REVERT: G 128 ARG cc_start: 0.8582 (tmm-80) cc_final: 0.8358 (ttt-90) REVERT: G 144 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7889 (mp0) REVERT: G 152 ARG cc_start: 0.6227 (ptm-80) cc_final: 0.5716 (mtm110) REVERT: G 203 LYS cc_start: 0.9282 (mmmt) cc_final: 0.8915 (mmtt) REVERT: G 317 PHE cc_start: 0.7910 (t80) cc_final: 0.7606 (m-80) outliers start: 89 outliers final: 47 residues processed: 311 average time/residue: 1.1548 time to fit residues: 407.8792 Evaluate side-chains 303 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 241 time to evaluate : 2.060 ------------------------------------------------------------------------------- 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 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 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 297 MET 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 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 272 VAL Chi-restraints excluded: chain D residue 276 ARG 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 240 PHE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 266 GLN 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 138 ASP 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 266 GLN 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 352 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 185 optimal weight: 0.0170 chunk 88 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 0.2980 chunk 114 optimal weight: 6.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- 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 282 ASN C 340 ASN C 355 ASN D 355 ASN E 340 ASN E 355 ASN F 282 ASN F 355 ASN G 56 GLN G 355 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.128040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.086375 restraints weight = 30564.492| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.48 r_work: 0.2997 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18732 Z= 0.113 Angle : 0.616 10.844 25473 Z= 0.292 Chirality : 0.039 0.194 3045 Planarity : 0.003 0.034 3052 Dihedral : 4.582 56.135 2438 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.85 % Allowed : 25.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.19), residues: 2198 helix: 2.55 (0.14), residues: 1512 sheet: 0.26 (0.48), residues: 126 loop : -1.11 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 104 HIS 0.002 0.000 HIS F 134 PHE 0.009 0.001 PHE F 12 TYR 0.021 0.001 TYR E 232 ARG 0.007 0.001 ARG F 29 Details of bonding type rmsd hydrogen bonds : bond 0.03126 ( 1142) hydrogen bonds : angle 3.62858 ( 3363) SS BOND : bond 0.00254 ( 14) SS BOND : angle 1.38325 ( 28) covalent geometry : bond 0.00250 (18718) covalent geometry : angle 0.61477 (25445) *********************** 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 324 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 245 time to evaluate : 2.004 Fit side-chains REVERT: A 14 ASP cc_start: 0.8395 (m-30) cc_final: 0.7606 (p0) REVERT: A 144 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8031 (mp0) REVERT: A 152 ARG cc_start: 0.6269 (ptm-80) cc_final: 0.5760 (mtm110) REVERT: A 240 PHE cc_start: 0.7521 (OUTLIER) cc_final: 0.6815 (m-80) REVERT: A 358 ASN cc_start: 0.8814 (t0) cc_final: 0.8448 (t0) REVERT: B 14 ASP cc_start: 0.8508 (m-30) cc_final: 0.7812 (p0) REVERT: B 144 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8012 (mp0) REVERT: B 152 ARG cc_start: 0.6165 (ptm-80) cc_final: 0.5672 (mtm110) REVERT: B 203 LYS cc_start: 0.9155 (mmmt) cc_final: 0.8800 (mmtt) REVERT: B 240 PHE cc_start: 0.7595 (OUTLIER) cc_final: 0.7283 (m-80) REVERT: B 266 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8044 (tt0) REVERT: B 306 ASN cc_start: 0.7543 (t0) cc_final: 0.7287 (t0) REVERT: B 358 ASN cc_start: 0.8871 (t0) cc_final: 0.8508 (t0) REVERT: C 14 ASP cc_start: 0.8446 (m-30) cc_final: 0.7636 (p0) REVERT: C 144 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.8024 (mp0) REVERT: C 152 ARG cc_start: 0.6078 (ptm-80) cc_final: 0.5623 (mtm110) REVERT: C 297 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.8107 (pmt) REVERT: C 306 ASN cc_start: 0.7784 (t0) cc_final: 0.7547 (t0) REVERT: C 352 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8577 (t) REVERT: D 14 ASP cc_start: 0.8286 (m-30) cc_final: 0.7583 (p0) REVERT: D 152 ARG cc_start: 0.6347 (ptm-80) cc_final: 0.5821 (mtm110) REVERT: D 200 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8375 (mm-40) REVERT: D 240 PHE cc_start: 0.7606 (OUTLIER) cc_final: 0.6327 (t80) REVERT: D 306 ASN cc_start: 0.7635 (t0) cc_final: 0.7378 (t0) REVERT: E 14 ASP cc_start: 0.8406 (m-30) cc_final: 0.7747 (p0) REVERT: E 144 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8038 (mp0) REVERT: E 152 ARG cc_start: 0.6222 (ptm-80) cc_final: 0.5716 (mtm110) REVERT: E 203 LYS cc_start: 0.9203 (mmmt) cc_final: 0.8909 (mptt) REVERT: E 266 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8045 (tt0) REVERT: E 306 ASN cc_start: 0.7575 (t0) cc_final: 0.7317 (t0) REVERT: F 14 ASP cc_start: 0.8470 (m-30) cc_final: 0.7841 (t0) REVERT: F 144 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8247 (mp0) REVERT: F 152 ARG cc_start: 0.6156 (ptm-80) cc_final: 0.5937 (ptm-80) REVERT: F 203 LYS cc_start: 0.9197 (mmmt) cc_final: 0.8869 (mptt) REVERT: F 266 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8101 (tt0) REVERT: F 280 TYR cc_start: 0.8145 (t80) cc_final: 0.7584 (m-80) REVERT: F 297 MET cc_start: 0.7888 (pmt) cc_final: 0.7610 (pmt) REVERT: F 358 ASN cc_start: 0.8976 (t0) cc_final: 0.8673 (t0) REVERT: G 14 ASP cc_start: 0.8403 (m-30) cc_final: 0.7706 (p0) REVERT: G 128 ARG cc_start: 0.8561 (tmm-80) cc_final: 0.8335 (ttt-90) REVERT: G 144 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7898 (mp0) REVERT: G 152 ARG cc_start: 0.6226 (ptm-80) cc_final: 0.5709 (mtm110) REVERT: G 203 LYS cc_start: 0.9269 (mmmt) cc_final: 0.8913 (mmtt) REVERT: G 317 PHE cc_start: 0.7907 (t80) cc_final: 0.7605 (m-80) outliers start: 79 outliers final: 52 residues processed: 305 average time/residue: 1.1251 time to fit residues: 390.4532 Evaluate side-chains 303 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 238 time to evaluate : 2.037 ------------------------------------------------------------------------------- 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 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 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 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 297 MET 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 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 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 266 GLN 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 255 LEU Chi-restraints excluded: chain F residue 266 GLN 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 352 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 121 optimal weight: 6.9990 chunk 223 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 182 optimal weight: 2.9990 chunk 65 optimal weight: 0.0060 chunk 118 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 222 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 155 optimal weight: 7.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- 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 340 ASN C 355 ASN D 355 ASN E 355 ASN F 282 ASN F 306 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 = 0.3788 r_free = 0.3788 target = 0.125291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.082921 restraints weight = 30814.002| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.49 r_work: 0.2932 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 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 : 0.004 0.038 18732 Z= 0.162 Angle : 0.660 12.781 25473 Z= 0.314 Chirality : 0.041 0.211 3045 Planarity : 0.003 0.029 3052 Dihedral : 4.792 59.909 2438 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 4.34 % Allowed : 25.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.19), residues: 2198 helix: 2.41 (0.14), residues: 1519 sheet: 0.34 (0.49), residues: 126 loop : -1.17 (0.29), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 85 HIS 0.004 0.001 HIS C 106 PHE 0.011 0.001 PHE A 333 TYR 0.032 0.001 TYR G 232 ARG 0.007 0.001 ARG D 29 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 1142) hydrogen bonds : angle 3.77934 ( 3363) SS BOND : bond 0.00171 ( 14) SS BOND : angle 1.54943 ( 28) covalent geometry : bond 0.00391 (18718) covalent geometry : angle 0.65850 (25445) *********************** 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 331 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 242 time to evaluate : 2.128 Fit side-chains REVERT: A 14 ASP cc_start: 0.8488 (m-30) cc_final: 0.7630 (p0) REVERT: A 144 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: A 152 ARG cc_start: 0.6235 (ptm-80) cc_final: 0.5714 (mtm110) REVERT: A 240 PHE cc_start: 0.7676 (OUTLIER) cc_final: 0.7072 (m-80) REVERT: A 358 ASN cc_start: 0.8826 (t0) cc_final: 0.8471 (t0) REVERT: B 14 ASP cc_start: 0.8506 (m-30) cc_final: 0.7825 (p0) REVERT: B 144 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8040 (mp0) REVERT: B 152 ARG cc_start: 0.6293 (ptm-80) cc_final: 0.5789 (mtm110) REVERT: B 203 LYS cc_start: 0.9172 (mmmt) cc_final: 0.8822 (mmtt) REVERT: B 240 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.7351 (m-80) REVERT: B 266 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8208 (tt0) REVERT: B 306 ASN cc_start: 0.7446 (t0) cc_final: 0.7166 (t0) REVERT: B 358 ASN cc_start: 0.8901 (t0) cc_final: 0.8542 (t0) REVERT: C 14 ASP cc_start: 0.8485 (m-30) cc_final: 0.7743 (p0) REVERT: C 144 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7991 (mp0) REVERT: C 152 ARG cc_start: 0.6087 (ptm-80) cc_final: 0.5608 (mtm110) REVERT: C 255 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8745 (pp) REVERT: C 297 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7955 (pmt) REVERT: C 306 ASN cc_start: 0.7661 (t0) cc_final: 0.7425 (t0) REVERT: D 14 ASP cc_start: 0.8343 (m-30) cc_final: 0.7615 (p0) REVERT: D 152 ARG cc_start: 0.6282 (ptm-80) cc_final: 0.5780 (mtm110) REVERT: D 200 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8392 (mm-40) REVERT: D 240 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.6372 (t80) REVERT: D 306 ASN cc_start: 0.7719 (t0) cc_final: 0.7404 (t0) REVERT: D 317 PHE cc_start: 0.7870 (OUTLIER) cc_final: 0.7496 (m-80) REVERT: E 14 ASP cc_start: 0.8444 (m-30) cc_final: 0.7799 (p0) REVERT: E 144 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8033 (mp0) REVERT: E 152 ARG cc_start: 0.6212 (ptm-80) cc_final: 0.5739 (mtm110) REVERT: E 200 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8402 (mm-40) REVERT: E 203 LYS cc_start: 0.9221 (mmmt) cc_final: 0.8922 (mptt) REVERT: E 266 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8191 (tt0) REVERT: E 306 ASN cc_start: 0.7546 (t0) cc_final: 0.7269 (t0) REVERT: F 14 ASP cc_start: 0.8544 (m-30) cc_final: 0.8032 (t0) REVERT: F 89 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7730 (tt0) REVERT: F 144 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8284 (mp0) REVERT: F 152 ARG cc_start: 0.6127 (ptm-80) cc_final: 0.5910 (ptm-80) REVERT: F 203 LYS cc_start: 0.9230 (mmmt) cc_final: 0.8896 (mptt) REVERT: F 266 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8290 (tt0) REVERT: F 280 TYR cc_start: 0.8163 (t80) cc_final: 0.7617 (m-80) REVERT: F 297 MET cc_start: 0.7906 (pmt) cc_final: 0.7663 (pmt) REVERT: F 306 ASN cc_start: 0.7658 (t0) cc_final: 0.7428 (t0) REVERT: F 358 ASN cc_start: 0.9030 (t0) cc_final: 0.8746 (t0) REVERT: G 14 ASP cc_start: 0.8479 (m-30) cc_final: 0.7782 (p0) REVERT: G 128 ARG cc_start: 0.8583 (tmm-80) cc_final: 0.8352 (ttt-90) REVERT: G 144 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7900 (mp0) REVERT: G 152 ARG cc_start: 0.6221 (ptm-80) cc_final: 0.5709 (mtm110) REVERT: G 200 GLN cc_start: 0.8183 (mp10) cc_final: 0.7981 (mp10) REVERT: G 203 LYS cc_start: 0.9288 (mmmt) cc_final: 0.8936 (mmtt) REVERT: G 317 PHE cc_start: 0.7942 (t80) cc_final: 0.7633 (m-80) outliers start: 89 outliers final: 50 residues processed: 311 average time/residue: 1.1427 time to fit residues: 404.3248 Evaluate side-chains 300 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 235 time to evaluate : 2.010 ------------------------------------------------------------------------------- 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 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 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 297 MET 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 317 PHE 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 202 LEU Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 89 GLN 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 255 LEU Chi-restraints excluded: chain F residue 266 GLN 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 352 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 55 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 120 optimal weight: 0.0170 chunk 107 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 21 optimal weight: 0.0050 chunk 80 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 63 optimal weight: 20.0000 overall best weight: 0.5234 ------------------------------------------------------------------------------- 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 340 ASN C 355 ASN D 355 ASN E 355 ASN G 355 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.128131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.086617 restraints weight = 30554.464| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.47 r_work: 0.2999 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18732 Z= 0.116 Angle : 0.646 12.097 25473 Z= 0.306 Chirality : 0.040 0.199 3045 Planarity : 0.003 0.031 3052 Dihedral : 4.683 57.384 2438 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.46 % Allowed : 26.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.19), residues: 2198 helix: 2.56 (0.14), residues: 1512 sheet: 0.37 (0.49), residues: 126 loop : -1.05 (0.29), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 74 HIS 0.001 0.000 HIS B 106 PHE 0.010 0.001 PHE F 12 TYR 0.029 0.001 TYR E 232 ARG 0.007 0.001 ARG D 29 Details of bonding type rmsd hydrogen bonds : bond 0.03094 ( 1142) hydrogen bonds : angle 3.68273 ( 3363) SS BOND : bond 0.00255 ( 14) SS BOND : angle 1.37536 ( 28) covalent geometry : bond 0.00256 (18718) covalent geometry : angle 0.64465 (25445) ********************** 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 319 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 248 time to evaluate : 2.109 Fit side-chains REVERT: A 14 ASP cc_start: 0.8469 (m-30) cc_final: 0.7527 (p0) REVERT: A 144 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7999 (mp0) REVERT: A 152 ARG cc_start: 0.6201 (ptm-80) cc_final: 0.5688 (mtm110) REVERT: A 240 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.6866 (m-80) REVERT: A 280 TYR cc_start: 0.8173 (t80) cc_final: 0.7581 (m-80) REVERT: A 358 ASN cc_start: 0.8831 (t0) cc_final: 0.8461 (t0) REVERT: B 14 ASP cc_start: 0.8491 (m-30) cc_final: 0.7809 (p0) REVERT: B 144 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7990 (mp0) REVERT: B 152 ARG cc_start: 0.6168 (ptm-80) cc_final: 0.5649 (mtm110) REVERT: B 203 LYS cc_start: 0.9161 (mmmt) cc_final: 0.8798 (mmtt) REVERT: B 240 PHE cc_start: 0.7557 (OUTLIER) cc_final: 0.7259 (m-80) REVERT: B 266 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8043 (tt0) REVERT: B 306 ASN cc_start: 0.7466 (t0) cc_final: 0.7191 (t0) REVERT: B 358 ASN cc_start: 0.8933 (t0) cc_final: 0.8530 (t0) REVERT: C 14 ASP cc_start: 0.8450 (m-30) cc_final: 0.7637 (p0) REVERT: C 144 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8023 (mp0) REVERT: C 152 ARG cc_start: 0.6085 (ptm-80) cc_final: 0.5598 (mtm110) REVERT: C 297 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8090 (pmt) REVERT: C 306 ASN cc_start: 0.7661 (t0) cc_final: 0.7403 (t0) REVERT: D 14 ASP cc_start: 0.8249 (m-30) cc_final: 0.7577 (p0) REVERT: D 152 ARG cc_start: 0.6352 (ptm-80) cc_final: 0.5828 (mtm110) REVERT: D 200 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8384 (mm-40) REVERT: D 240 PHE cc_start: 0.7657 (OUTLIER) cc_final: 0.6296 (t80) REVERT: D 306 ASN cc_start: 0.7710 (t0) cc_final: 0.7383 (t0) REVERT: E 14 ASP cc_start: 0.8409 (m-30) cc_final: 0.7763 (p0) REVERT: E 144 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7993 (mp0) REVERT: E 152 ARG cc_start: 0.6228 (ptm-80) cc_final: 0.5734 (mtm110) REVERT: E 203 LYS cc_start: 0.9215 (mmmt) cc_final: 0.8912 (mptt) REVERT: E 266 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8037 (tt0) REVERT: E 306 ASN cc_start: 0.7522 (t0) cc_final: 0.7307 (t0) REVERT: F 14 ASP cc_start: 0.8488 (m-30) cc_final: 0.7824 (t70) REVERT: F 144 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8268 (mp0) REVERT: F 152 ARG cc_start: 0.6130 (ptm-80) cc_final: 0.5915 (ptm-80) REVERT: F 203 LYS cc_start: 0.9222 (mmmt) cc_final: 0.8891 (mptt) REVERT: F 280 TYR cc_start: 0.8084 (t80) cc_final: 0.7567 (m-80) REVERT: F 306 ASN cc_start: 0.7574 (t0) cc_final: 0.7370 (t0) REVERT: F 358 ASN cc_start: 0.9064 (t0) cc_final: 0.8776 (t0) REVERT: G 14 ASP cc_start: 0.8424 (m-30) cc_final: 0.7727 (p0) REVERT: G 128 ARG cc_start: 0.8564 (tmm-80) cc_final: 0.8336 (ttt-90) REVERT: G 144 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7928 (mp0) REVERT: G 152 ARG cc_start: 0.6177 (ptm-80) cc_final: 0.5704 (mtm110) REVERT: G 200 GLN cc_start: 0.8179 (mp10) cc_final: 0.7959 (mp10) REVERT: G 266 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8264 (tt0) REVERT: G 317 PHE cc_start: 0.7913 (t80) cc_final: 0.7611 (m-80) outliers start: 71 outliers final: 50 residues processed: 303 average time/residue: 1.3164 time to fit residues: 460.3024 Evaluate side-chains 302 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 240 time to evaluate : 2.142 ------------------------------------------------------------------------------- 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 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 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 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 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 297 MET 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 255 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 276 ARG 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 266 GLN 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 255 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 352 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 78 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 199 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 217 optimal weight: 0.2980 chunk 204 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 340 ASN C 355 ASN D 355 ASN E 355 ASN F 355 ASN G 306 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 = 0.3815 r_free = 0.3815 target = 0.127375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.085986 restraints weight = 30528.286| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.45 r_work: 0.2985 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18732 Z= 0.124 Angle : 0.667 13.571 25473 Z= 0.314 Chirality : 0.040 0.215 3045 Planarity : 0.003 0.032 3052 Dihedral : 4.503 55.956 2438 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.61 % Allowed : 26.28 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.19), residues: 2198 helix: 2.53 (0.14), residues: 1519 sheet: 0.41 (0.49), residues: 126 loop : -1.05 (0.29), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 127 HIS 0.002 0.001 HIS B 106 PHE 0.009 0.001 PHE D 12 TYR 0.025 0.001 TYR E 232 ARG 0.008 0.001 ARG C 29 Details of bonding type rmsd hydrogen bonds : bond 0.03178 ( 1142) hydrogen bonds : angle 3.72007 ( 3363) SS BOND : bond 0.00225 ( 14) SS BOND : angle 1.40748 ( 28) covalent geometry : bond 0.00287 (18718) covalent geometry : angle 0.66553 (25445) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13637.99 seconds wall clock time: 239 minutes 3.26 seconds (14343.26 seconds total)