Starting phenix.real_space_refine on Mon May 19 05:14:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bz8_45056/05_2025/9bz8_45056.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bz8_45056/05_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_45056/05_2025/9bz8_45056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bz8_45056/05_2025/9bz8_45056.map" model { file = "/net/cci-nas-00/data/ceres_data/9bz8_45056/05_2025/9bz8_45056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bz8_45056/05_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 6.18, per 1000 atoms: 0.34 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: 4.42 Conformation dependent library (CDL) restraints added in 2.1 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: 1.78 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: 4.75 Time building geometry restraints manager: 5.15 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: 0.15 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: 0.630 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: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 34.020 Find NCS groups from input model: 0.360 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:12.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.450 ------------------------------------------------------------------------------- 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 : 2.124 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: 1.3114 time to fit residues: 607.0921 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 : 1.978 ------------------------------------------------------------------------------- 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 = 0.3779 r_free = 0.3779 target = 0.124328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.081962 restraints weight = 30938.729| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.45 r_work: 0.2909 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 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 2.09237 ( 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 : 2.255 Fit side-chains revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8469 (m-30) cc_final: 0.7982 (t0) REVERT: A 124 ASN cc_start: 0.8189 (OUTLIER) cc_final: 0.7871 (p0) REVERT: A 144 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.8049 (mp0) REVERT: A 152 ARG cc_start: 0.6205 (ptm-80) cc_final: 0.5801 (mtm110) REVERT: A 240 PHE cc_start: 0.7620 (OUTLIER) cc_final: 0.7102 (m-80) REVERT: A 358 ASN cc_start: 0.8792 (t0) cc_final: 0.8448 (t0) REVERT: B 14 ASP cc_start: 0.8664 (m-30) cc_final: 0.7832 (p0) REVERT: B 124 ASN cc_start: 0.8327 (OUTLIER) cc_final: 0.8067 (p0) REVERT: B 144 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8095 (mp0) REVERT: B 152 ARG cc_start: 0.6164 (ptm-80) cc_final: 0.5725 (mtm110) REVERT: B 240 PHE cc_start: 0.7597 (OUTLIER) cc_final: 0.7291 (m-80) REVERT: B 306 ASN cc_start: 0.7414 (t0) cc_final: 0.7213 (t0) REVERT: B 317 PHE cc_start: 0.7793 (t80) cc_final: 0.7373 (m-80) REVERT: B 358 ASN cc_start: 0.8823 (t0) cc_final: 0.8436 (t0) REVERT: C 14 ASP cc_start: 0.8605 (m-30) cc_final: 0.7840 (p0) REVERT: C 124 ASN cc_start: 0.8277 (OUTLIER) cc_final: 0.7976 (p0) REVERT: C 152 ARG cc_start: 0.6051 (ptm-80) cc_final: 0.5715 (mtm110) REVERT: C 297 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7574 (pmm) REVERT: D 14 ASP cc_start: 0.8350 (m-30) cc_final: 0.7607 (p0) REVERT: D 124 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.7936 (p0) REVERT: D 152 ARG cc_start: 0.6173 (ptm-80) cc_final: 0.5750 (mtm110) REVERT: D 306 ASN cc_start: 0.7671 (t0) cc_final: 0.7445 (t0) REVERT: E 14 ASP cc_start: 0.8566 (m-30) cc_final: 0.7800 (p0) REVERT: E 144 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7941 (mp0) REVERT: E 152 ARG cc_start: 0.6129 (ptm-80) cc_final: 0.5711 (mtm110) REVERT: E 200 GLN cc_start: 0.8874 (mm-40) cc_final: 0.8276 (mm-40) REVERT: E 297 MET cc_start: 0.7876 (pmm) cc_final: 0.7599 (pmm) REVERT: E 306 ASN cc_start: 0.7563 (t0) cc_final: 0.7277 (t0) REVERT: F 14 ASP cc_start: 0.8503 (m-30) cc_final: 0.7833 (t0) REVERT: F 152 ARG cc_start: 0.6215 (ptm-80) cc_final: 0.5952 (mtp-110) REVERT: F 358 ASN cc_start: 0.8863 (t0) cc_final: 0.8588 (t0) REVERT: G 14 ASP cc_start: 0.8593 (m-30) cc_final: 0.7869 (p0) REVERT: G 144 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7922 (mp0) REVERT: G 152 ARG cc_start: 0.6117 (ptm-80) cc_final: 0.5647 (mtm110) REVERT: G 317 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.7588 (m-80) outliers start: 140 outliers final: 47 residues processed: 363 average time/residue: 1.1246 time to fit residues: 462.3969 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 : 1.954 ------------------------------------------------------------------------------- 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: 10.0000 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: 1.9990 chunk 164 optimal weight: 0.9980 chunk 210 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3802 r_free = 0.3802 target = 0.126242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.084497 restraints weight = 30624.640| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.44 r_work: 0.2956 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18732 Z= 0.129 Angle : 0.588 8.004 25473 Z= 0.283 Chirality : 0.039 0.176 3045 Planarity : 0.003 0.028 3052 Dihedral : 4.496 52.426 2444 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 5.56 % Allowed : 24.09 % Favored : 70.36 % 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: 2.47 (0.13), residues: 1519 sheet: -0.11 (0.47), residues: 126 loop : -1.36 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 85 HIS 0.003 0.001 HIS B 106 PHE 0.011 0.001 PHE E 83 TYR 0.022 0.001 TYR E 232 ARG 0.005 0.001 ARG F 29 Details of bonding type rmsd hydrogen bonds : bond 0.03581 ( 1142) hydrogen bonds : angle 3.76037 ( 3363) SS BOND : bond 0.00133 ( 14) SS BOND : angle 1.69370 ( 28) covalent geometry : bond 0.00302 (18718) covalent geometry : angle 0.58595 (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 370 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 256 time to evaluate : 2.278 Fit side-chains revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8440 (m-30) cc_final: 0.7977 (t0) REVERT: A 124 ASN cc_start: 0.8106 (OUTLIER) cc_final: 0.7797 (p0) REVERT: A 144 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7988 (mp0) REVERT: A 152 ARG cc_start: 0.6224 (ptm-80) cc_final: 0.5744 (mtm110) REVERT: A 240 PHE cc_start: 0.7649 (OUTLIER) cc_final: 0.7122 (m-80) REVERT: A 358 ASN cc_start: 0.8802 (t0) cc_final: 0.8458 (t0) REVERT: B 14 ASP cc_start: 0.8599 (m-30) cc_final: 0.7801 (p0) REVERT: B 124 ASN cc_start: 0.8310 (OUTLIER) cc_final: 0.8015 (p0) REVERT: B 144 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7986 (mp0) REVERT: B 152 ARG cc_start: 0.6186 (ptm-80) cc_final: 0.5700 (mtm110) REVERT: B 240 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.7326 (m-80) REVERT: B 306 ASN cc_start: 0.7540 (t0) cc_final: 0.7071 (t0) REVERT: B 358 ASN cc_start: 0.8830 (t0) cc_final: 0.8445 (t0) REVERT: C 124 ASN cc_start: 0.8252 (OUTLIER) cc_final: 0.7972 (p0) REVERT: C 152 ARG cc_start: 0.6043 (ptm-80) cc_final: 0.5634 (mtm110) REVERT: D 14 ASP cc_start: 0.8303 (m-30) cc_final: 0.7585 (p0) REVERT: D 124 ASN cc_start: 0.8214 (OUTLIER) cc_final: 0.7955 (p0) REVERT: D 152 ARG cc_start: 0.6190 (ptm-80) cc_final: 0.5692 (mtm110) REVERT: D 240 PHE cc_start: 0.7610 (OUTLIER) cc_final: 0.6355 (t80) REVERT: D 306 ASN cc_start: 0.7552 (t0) cc_final: 0.7295 (t0) REVERT: E 14 ASP cc_start: 0.8500 (m-30) cc_final: 0.7741 (p0) REVERT: E 144 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7900 (mp0) REVERT: E 152 ARG cc_start: 0.6229 (ptm-80) cc_final: 0.5778 (mtm110) REVERT: E 203 LYS cc_start: 0.9275 (mmmt) cc_final: 0.8841 (mmtt) REVERT: E 297 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7695 (pmm) REVERT: E 306 ASN cc_start: 0.7566 (t0) cc_final: 0.7187 (t0) REVERT: F 9 GLU cc_start: 0.8435 (tt0) cc_final: 0.8119 (tt0) REVERT: F 14 ASP cc_start: 0.8491 (m-30) cc_final: 0.7817 (t0) REVERT: F 124 ASN cc_start: 0.8119 (OUTLIER) cc_final: 0.7822 (p0) REVERT: F 144 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8162 (mp0) REVERT: F 152 ARG cc_start: 0.6199 (ptm-80) cc_final: 0.5813 (mtm110) REVERT: F 266 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8113 (tt0) REVERT: F 338 GLU cc_start: 0.8887 (tt0) cc_final: 0.8361 (tp30) REVERT: F 340 ASN cc_start: 0.8993 (OUTLIER) cc_final: 0.8749 (t0) REVERT: F 354 GLU cc_start: 0.9052 (tp30) cc_final: 0.8645 (tp30) REVERT: F 358 ASN cc_start: 0.8862 (t0) cc_final: 0.8612 (t0) REVERT: G 14 ASP cc_start: 0.8539 (m-30) cc_final: 0.7737 (p0) REVERT: G 128 ARG cc_start: 0.8642 (tmm-80) cc_final: 0.8362 (ttt-90) REVERT: G 144 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7796 (mp0) REVERT: G 152 ARG cc_start: 0.6222 (ptm-80) cc_final: 0.5692 (mtm110) outliers start: 114 outliers final: 43 residues processed: 340 average time/residue: 1.0805 time to fit residues: 419.7223 Evaluate side-chains 297 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 239 time to evaluate : 1.946 ------------------------------------------------------------------------------- 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 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 352 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain 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 138 ASP 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: 9.9990 chunk 133 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 0.0470 overall best weight: 1.1884 ------------------------------------------------------------------------------- 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 = 0.3802 r_free = 0.3802 target = 0.126404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.084992 restraints weight = 30570.933| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.44 r_work: 0.2969 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2297 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= 0.124 Angle : 0.598 8.810 25473 Z= 0.285 Chirality : 0.039 0.175 3045 Planarity : 0.003 0.027 3052 Dihedral : 4.528 53.333 2443 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 5.07 % Allowed : 24.04 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.16 (0.19), residues: 2198 helix: 2.48 (0.13), residues: 1512 sheet: -0.01 (0.47), residues: 126 loop : -1.28 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 85 HIS 0.003 0.001 HIS B 106 PHE 0.010 0.001 PHE D 12 TYR 0.024 0.001 TYR E 232 ARG 0.006 0.001 ARG D 29 Details of bonding type rmsd hydrogen bonds : bond 0.03457 ( 1142) hydrogen bonds : angle 3.71913 ( 3363) SS BOND : bond 0.00160 ( 14) SS BOND : angle 1.53762 ( 28) covalent geometry : bond 0.00289 (18718) covalent geometry : angle 0.59637 (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 346 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 242 time to evaluate : 2.199 Fit side-chains REVERT: A 14 ASP cc_start: 0.8577 (m-30) cc_final: 0.8025 (t0) REVERT: A 124 ASN cc_start: 0.8214 (OUTLIER) cc_final: 0.7841 (p0) REVERT: A 144 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8126 (mp0) REVERT: A 152 ARG cc_start: 0.6346 (ptm-80) cc_final: 0.5832 (mtm110) REVERT: A 240 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.7213 (m-80) REVERT: A 358 ASN cc_start: 0.8821 (t0) cc_final: 0.8487 (t0) REVERT: B 14 ASP cc_start: 0.8681 (m-30) cc_final: 0.7857 (p0) REVERT: B 124 ASN cc_start: 0.8439 (OUTLIER) cc_final: 0.8104 (p0) REVERT: B 144 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8115 (mp0) REVERT: B 152 ARG cc_start: 0.6213 (ptm-80) cc_final: 0.5746 (mtm110) REVERT: B 203 LYS cc_start: 0.9174 (mmmt) cc_final: 0.8749 (mmtt) REVERT: B 240 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.7415 (m-80) REVERT: B 317 PHE cc_start: 0.7740 (t80) cc_final: 0.7348 (m-80) REVERT: B 358 ASN cc_start: 0.8852 (t0) cc_final: 0.8462 (t0) REVERT: C 14 ASP cc_start: 0.8576 (m-30) cc_final: 0.7629 (p0) REVERT: C 124 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.8071 (p0) REVERT: C 144 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: C 152 ARG cc_start: 0.6101 (ptm-80) cc_final: 0.5654 (mtm110) REVERT: C 297 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7911 (pmt) REVERT: C 306 ASN cc_start: 0.7395 (t0) cc_final: 0.7106 (t0) REVERT: C 352 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8503 (t) REVERT: D 14 ASP cc_start: 0.8433 (m-30) cc_final: 0.7633 (p0) REVERT: D 124 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.8113 (p0) REVERT: D 152 ARG cc_start: 0.6255 (ptm-80) cc_final: 0.5760 (mtm110) REVERT: D 240 PHE cc_start: 0.7746 (OUTLIER) cc_final: 0.6524 (t80) REVERT: D 306 ASN cc_start: 0.7620 (t0) cc_final: 0.7320 (t0) REVERT: D 317 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7640 (m-80) REVERT: E 14 ASP cc_start: 0.8607 (m-30) cc_final: 0.7865 (p0) REVERT: E 144 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8029 (mp0) REVERT: E 152 ARG cc_start: 0.6294 (ptm-80) cc_final: 0.5831 (mtm110) REVERT: E 203 LYS cc_start: 0.9300 (mmmt) cc_final: 0.8845 (mmtt) REVERT: E 297 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7784 (pmm) REVERT: E 306 ASN cc_start: 0.7557 (t0) cc_final: 0.7297 (t0) REVERT: F 14 ASP cc_start: 0.8680 (m-30) cc_final: 0.7866 (t0) REVERT: F 124 ASN cc_start: 0.8225 (OUTLIER) cc_final: 0.7894 (p0) REVERT: F 152 ARG cc_start: 0.6240 (ptm-80) cc_final: 0.5843 (mtm110) REVERT: F 203 LYS cc_start: 0.9189 (mmmt) cc_final: 0.8839 (mptt) REVERT: F 266 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8227 (tt0) REVERT: F 358 ASN cc_start: 0.8889 (t0) cc_final: 0.8621 (t0) REVERT: G 14 ASP cc_start: 0.8593 (m-30) cc_final: 0.7735 (p0) REVERT: G 128 ARG cc_start: 0.8719 (tmm-80) cc_final: 0.8455 (ttt-90) REVERT: G 144 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7952 (mp0) REVERT: G 152 ARG cc_start: 0.6270 (ptm-80) cc_final: 0.5724 (mtm110) REVERT: G 203 LYS cc_start: 0.9262 (mmmt) cc_final: 0.8844 (mmtt) REVERT: G 317 PHE cc_start: 0.7914 (t80) cc_final: 0.7557 (m-80) outliers start: 104 outliers final: 47 residues processed: 319 average time/residue: 1.0795 time to fit residues: 393.4357 Evaluate side-chains 302 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 237 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 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 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 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 56 optimal weight: 0.9980 chunk 194 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 184 optimal weight: 0.9990 chunk 218 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 174 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 340 ASN E 355 ASN F 282 ASN F 306 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 = 0.3797 r_free = 0.3797 target = 0.126077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.084313 restraints weight = 30683.033| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.47 r_work: 0.2955 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18732 Z= 0.134 Angle : 0.602 8.308 25473 Z= 0.286 Chirality : 0.039 0.179 3045 Planarity : 0.003 0.028 3052 Dihedral : 4.326 53.784 2438 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 5.51 % Allowed : 23.65 % 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: 2.16 (0.19), residues: 2198 helix: 2.43 (0.13), residues: 1519 sheet: 0.13 (0.48), residues: 126 loop : -1.21 (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 A 106 PHE 0.010 0.001 PHE D 12 TYR 0.027 0.001 TYR F 232 ARG 0.006 0.000 ARG D 29 Details of bonding type rmsd hydrogen bonds : bond 0.03472 ( 1142) hydrogen bonds : angle 3.70584 ( 3363) SS BOND : bond 0.00164 ( 14) SS BOND : angle 1.50614 ( 28) covalent geometry : bond 0.00318 (18718) covalent geometry : angle 0.60042 (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 358 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 245 time to evaluate : 2.371 Fit side-chains REVERT: A 14 ASP cc_start: 0.8488 (m-30) cc_final: 0.7606 (p0) REVERT: A 124 ASN cc_start: 0.8159 (OUTLIER) cc_final: 0.7768 (p0) REVERT: A 144 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.8001 (mp0) REVERT: A 152 ARG cc_start: 0.6280 (ptm-80) cc_final: 0.5787 (mtm110) REVERT: A 240 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.7109 (m-80) REVERT: A 358 ASN cc_start: 0.8816 (t0) cc_final: 0.8466 (t0) REVERT: B 14 ASP cc_start: 0.8553 (m-30) cc_final: 0.7806 (p0) REVERT: B 124 ASN cc_start: 0.8327 (OUTLIER) cc_final: 0.7927 (p0) REVERT: B 144 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7952 (mp0) REVERT: B 152 ARG cc_start: 0.6224 (ptm-80) cc_final: 0.5775 (mtm110) REVERT: B 203 LYS cc_start: 0.9189 (mmmt) cc_final: 0.8768 (mmtt) REVERT: B 240 PHE cc_start: 0.7658 (OUTLIER) cc_final: 0.7331 (m-80) REVERT: B 306 ASN cc_start: 0.7495 (t0) cc_final: 0.7253 (t0) REVERT: B 358 ASN cc_start: 0.8864 (t0) cc_final: 0.8463 (t0) REVERT: C 14 ASP cc_start: 0.8459 (m-30) cc_final: 0.7619 (p0) REVERT: C 124 ASN cc_start: 0.8322 (OUTLIER) cc_final: 0.8009 (p0) REVERT: C 144 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7990 (mp0) REVERT: C 152 ARG cc_start: 0.6048 (ptm-80) cc_final: 0.5612 (mtm110) REVERT: C 297 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7900 (pmt) REVERT: C 306 ASN cc_start: 0.7503 (t0) cc_final: 0.7247 (t0) REVERT: D 14 ASP cc_start: 0.8296 (m-30) cc_final: 0.7576 (p0) REVERT: D 124 ASN cc_start: 0.8298 (OUTLIER) cc_final: 0.7965 (p0) REVERT: D 152 ARG cc_start: 0.6210 (ptm-80) cc_final: 0.5722 (mtm110) REVERT: D 240 PHE cc_start: 0.7684 (OUTLIER) cc_final: 0.6344 (t80) REVERT: D 306 ASN cc_start: 0.7594 (t0) cc_final: 0.7315 (t0) REVERT: E 14 ASP cc_start: 0.8494 (m-30) cc_final: 0.7802 (p0) REVERT: E 144 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7905 (mp0) REVERT: E 152 ARG cc_start: 0.6227 (ptm-80) cc_final: 0.5751 (mtm110) REVERT: E 203 LYS cc_start: 0.9293 (mmmt) cc_final: 0.8866 (mmtt) REVERT: E 266 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8135 (tt0) REVERT: E 306 ASN cc_start: 0.7582 (t0) cc_final: 0.7327 (t0) REVERT: F 14 ASP cc_start: 0.8559 (m-30) cc_final: 0.7841 (t0) REVERT: F 144 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8200 (mp0) REVERT: F 152 ARG cc_start: 0.6121 (ptm-80) cc_final: 0.5710 (mtm110) REVERT: F 203 LYS cc_start: 0.9216 (mmmt) cc_final: 0.8858 (mptt) REVERT: F 232 TYR cc_start: 0.7756 (t80) cc_final: 0.7451 (t80) REVERT: F 266 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8131 (tt0) REVERT: F 297 MET cc_start: 0.7996 (pmt) cc_final: 0.7748 (pmt) REVERT: F 306 ASN cc_start: 0.7570 (t0) cc_final: 0.7353 (t0) REVERT: F 358 ASN cc_start: 0.8913 (t0) cc_final: 0.8634 (t0) REVERT: G 14 ASP cc_start: 0.8461 (m-30) cc_final: 0.7698 (p0) REVERT: G 128 ARG cc_start: 0.8590 (tmm-80) cc_final: 0.8293 (ttt180) REVERT: G 144 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7833 (mp0) REVERT: G 152 ARG cc_start: 0.6238 (ptm-80) cc_final: 0.5706 (mtm110) REVERT: G 203 LYS cc_start: 0.9236 (mmmt) cc_final: 0.8833 (mmtt) REVERT: G 317 PHE cc_start: 0.7896 (t80) cc_final: 0.7584 (m-80) outliers start: 113 outliers final: 56 residues processed: 336 average time/residue: 1.0629 time to fit residues: 409.1114 Evaluate side-chains 312 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 241 time to evaluate : 2.066 ------------------------------------------------------------------------------- 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 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 352 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 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 138 ASP 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 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 352 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 124 ASN Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 163 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 221 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 210 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 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 = 0.3785 r_free = 0.3785 target = 0.125229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.083240 restraints weight = 30707.169| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.46 r_work: 0.2934 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18732 Z= 0.156 Angle : 0.621 8.286 25473 Z= 0.296 Chirality : 0.040 0.194 3045 Planarity : 0.003 0.030 3052 Dihedral : 4.412 53.981 2438 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 5.56 % Allowed : 23.40 % Favored : 71.04 % 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: 2.40 (0.14), residues: 1512 sheet: 0.24 (0.48), residues: 126 loop : -1.29 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 85 HIS 0.003 0.001 HIS F 106 PHE 0.010 0.001 PHE D 12 TYR 0.027 0.001 TYR E 232 ARG 0.006 0.000 ARG F 29 Details of bonding type rmsd hydrogen bonds : bond 0.03622 ( 1142) hydrogen bonds : angle 3.75763 ( 3363) SS BOND : bond 0.00142 ( 14) SS BOND : angle 1.54889 ( 28) covalent geometry : bond 0.00379 (18718) covalent geometry : angle 0.61871 (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 357 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 243 time to evaluate : 2.062 Fit side-chains REVERT: A 14 ASP cc_start: 0.8492 (m-30) cc_final: 0.7649 (p0) REVERT: A 124 ASN cc_start: 0.8183 (OUTLIER) cc_final: 0.7779 (p0) REVERT: A 144 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: A 152 ARG cc_start: 0.6259 (ptm-80) cc_final: 0.5755 (mtm110) REVERT: A 240 PHE cc_start: 0.7704 (OUTLIER) cc_final: 0.7176 (m-80) REVERT: A 358 ASN cc_start: 0.8810 (t0) cc_final: 0.8445 (t0) REVERT: B 14 ASP cc_start: 0.8557 (m-30) cc_final: 0.7814 (p0) REVERT: B 144 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7987 (mp0) REVERT: B 152 ARG cc_start: 0.6233 (ptm-80) cc_final: 0.5774 (mtm110) REVERT: B 203 LYS cc_start: 0.9168 (mmmt) cc_final: 0.8748 (mmtt) REVERT: B 240 PHE cc_start: 0.7678 (OUTLIER) cc_final: 0.7428 (m-80) REVERT: B 266 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8182 (tt0) REVERT: B 306 ASN cc_start: 0.7547 (t0) cc_final: 0.7288 (t0) REVERT: B 317 PHE cc_start: 0.7823 (t80) cc_final: 0.7459 (m-80) REVERT: B 358 ASN cc_start: 0.8853 (t0) cc_final: 0.8471 (t0) REVERT: C 14 ASP cc_start: 0.8476 (m-30) cc_final: 0.7718 (p0) REVERT: C 124 ASN cc_start: 0.8298 (OUTLIER) cc_final: 0.7911 (p0) REVERT: C 144 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: C 152 ARG cc_start: 0.6062 (ptm-80) cc_final: 0.5611 (mtm110) REVERT: C 200 GLN cc_start: 0.8598 (mm-40) cc_final: 0.8372 (mm-40) REVERT: C 297 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7988 (pmt) REVERT: C 306 ASN cc_start: 0.7580 (t0) cc_final: 0.7294 (t0) REVERT: D 14 ASP cc_start: 0.8303 (m-30) cc_final: 0.7596 (p0) REVERT: D 124 ASN cc_start: 0.8268 (OUTLIER) cc_final: 0.7859 (p0) REVERT: D 152 ARG cc_start: 0.6296 (ptm-80) cc_final: 0.5799 (mtm110) REVERT: D 240 PHE cc_start: 0.7744 (OUTLIER) cc_final: 0.6371 (t80) REVERT: D 266 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8213 (tp-100) REVERT: D 306 ASN cc_start: 0.7614 (t0) cc_final: 0.7327 (t0) REVERT: D 317 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7582 (m-80) REVERT: E 14 ASP cc_start: 0.8471 (m-30) cc_final: 0.7777 (p0) REVERT: E 144 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7923 (mp0) REVERT: E 152 ARG cc_start: 0.6206 (ptm-80) cc_final: 0.5748 (mtm110) REVERT: E 203 LYS cc_start: 0.9267 (mmmt) cc_final: 0.8931 (mptt) REVERT: E 266 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8150 (tt0) REVERT: E 306 ASN cc_start: 0.7615 (t0) cc_final: 0.7351 (t0) REVERT: F 14 ASP cc_start: 0.8552 (m-30) cc_final: 0.7844 (t0) REVERT: F 144 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8239 (mp0) REVERT: F 152 ARG cc_start: 0.6139 (ptm-80) cc_final: 0.5753 (mtm110) REVERT: F 203 LYS cc_start: 0.9229 (mmmt) cc_final: 0.8880 (mptt) REVERT: F 266 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8244 (tt0) REVERT: F 297 MET cc_start: 0.8007 (pmt) cc_final: 0.7769 (pmt) REVERT: F 306 ASN cc_start: 0.7582 (t0) cc_final: 0.7360 (t0) REVERT: F 358 ASN cc_start: 0.8965 (t0) cc_final: 0.8679 (t0) REVERT: G 14 ASP cc_start: 0.8455 (m-30) cc_final: 0.7718 (p0) REVERT: G 128 ARG cc_start: 0.8652 (tmm-80) cc_final: 0.8363 (ttt180) REVERT: G 144 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: G 152 ARG cc_start: 0.6189 (ptm-80) cc_final: 0.5689 (mtm110) REVERT: G 203 LYS cc_start: 0.9232 (mmmt) cc_final: 0.8881 (mmtt) REVERT: G 266 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8226 (tt0) REVERT: G 317 PHE cc_start: 0.7906 (t80) cc_final: 0.7596 (m-80) outliers start: 114 outliers final: 57 residues processed: 334 average time/residue: 1.0267 time to fit residues: 392.5913 Evaluate side-chains 313 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 238 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 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 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 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 317 PHE Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 124 ASN Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 164 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 213 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 181 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 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 = 0.126110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.084111 restraints weight = 30549.555| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.47 r_work: 0.2956 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18732 Z= 0.131 Angle : 0.612 9.337 25473 Z= 0.291 Chirality : 0.039 0.188 3045 Planarity : 0.003 0.030 3052 Dihedral : 4.488 54.446 2438 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 5.27 % Allowed : 23.94 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.45 (0.14), residues: 1512 sheet: 0.30 (0.48), residues: 126 loop : -1.22 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 85 HIS 0.003 0.001 HIS E 106 PHE 0.010 0.001 PHE D 12 TYR 0.027 0.001 TYR E 232 ARG 0.006 0.000 ARG F 29 Details of bonding type rmsd hydrogen bonds : bond 0.03420 ( 1142) hydrogen bonds : angle 3.71553 ( 3363) SS BOND : bond 0.00205 ( 14) SS BOND : angle 1.50811 ( 28) covalent geometry : bond 0.00307 (18718) covalent geometry : angle 0.61058 (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 355 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 247 time to evaluate : 2.127 Fit side-chains REVERT: A 14 ASP cc_start: 0.8474 (m-30) cc_final: 0.7609 (p0) REVERT: A 124 ASN cc_start: 0.8239 (OUTLIER) cc_final: 0.7767 (p0) REVERT: A 144 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8032 (mp0) REVERT: A 152 ARG cc_start: 0.6275 (ptm-80) cc_final: 0.5784 (mtm110) REVERT: A 240 PHE cc_start: 0.7678 (OUTLIER) cc_final: 0.7195 (m-80) REVERT: A 358 ASN cc_start: 0.8817 (t0) cc_final: 0.8458 (t0) REVERT: B 14 ASP cc_start: 0.8523 (m-30) cc_final: 0.7811 (p0) REVERT: B 144 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7969 (mp0) REVERT: B 152 ARG cc_start: 0.6239 (ptm-80) cc_final: 0.5741 (mtm110) REVERT: B 203 LYS cc_start: 0.9152 (mmmt) cc_final: 0.8754 (mmtt) REVERT: B 240 PHE cc_start: 0.7634 (OUTLIER) cc_final: 0.7388 (m-80) REVERT: B 266 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8124 (tt0) REVERT: B 306 ASN cc_start: 0.7534 (t0) cc_final: 0.7255 (t0) REVERT: B 317 PHE cc_start: 0.7822 (t80) cc_final: 0.7487 (m-80) REVERT: B 358 ASN cc_start: 0.8855 (t0) cc_final: 0.8489 (t0) REVERT: C 14 ASP cc_start: 0.8468 (m-30) cc_final: 0.7720 (p0) REVERT: C 144 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7973 (mp0) REVERT: C 152 ARG cc_start: 0.6077 (ptm-80) cc_final: 0.5636 (mtm110) REVERT: C 200 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8380 (mm-40) REVERT: C 306 ASN cc_start: 0.7606 (t0) cc_final: 0.7322 (t0) REVERT: C 352 VAL cc_start: 0.8796 (OUTLIER) cc_final: 0.8574 (t) REVERT: D 14 ASP cc_start: 0.8286 (m-30) cc_final: 0.7592 (p0) REVERT: D 124 ASN cc_start: 0.8238 (OUTLIER) cc_final: 0.7774 (p0) REVERT: D 152 ARG cc_start: 0.6314 (ptm-80) cc_final: 0.5816 (mtm110) REVERT: D 240 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.6375 (t80) REVERT: D 266 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8346 (tt0) REVERT: D 306 ASN cc_start: 0.7638 (t0) cc_final: 0.7343 (t0) REVERT: D 317 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.7597 (m-80) REVERT: E 14 ASP cc_start: 0.8461 (m-30) cc_final: 0.7796 (p0) REVERT: E 144 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7982 (mp0) REVERT: E 152 ARG cc_start: 0.6223 (ptm-80) cc_final: 0.5730 (mtm110) REVERT: E 203 LYS cc_start: 0.9230 (mmmt) cc_final: 0.8905 (mptt) REVERT: E 266 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8130 (tt0) REVERT: E 306 ASN cc_start: 0.7561 (t0) cc_final: 0.7268 (t0) REVERT: F 14 ASP cc_start: 0.8535 (m-30) cc_final: 0.7967 (t0) REVERT: F 144 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8210 (mp0) REVERT: F 152 ARG cc_start: 0.6158 (ptm-80) cc_final: 0.5746 (mtm110) REVERT: F 203 LYS cc_start: 0.9220 (mmmt) cc_final: 0.8881 (mptt) REVERT: F 266 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8207 (tt0) REVERT: F 280 TYR cc_start: 0.8146 (t80) cc_final: 0.7605 (m-80) REVERT: F 306 ASN cc_start: 0.7601 (t0) cc_final: 0.7370 (t0) REVERT: F 358 ASN cc_start: 0.8986 (t0) cc_final: 0.8696 (t0) REVERT: G 14 ASP cc_start: 0.8426 (m-30) cc_final: 0.7708 (p0) REVERT: G 128 ARG cc_start: 0.8601 (tmm-80) cc_final: 0.8381 (ttt-90) REVERT: G 144 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7909 (mp0) REVERT: G 152 ARG cc_start: 0.6208 (ptm-80) cc_final: 0.5700 (mtm110) REVERT: G 203 LYS cc_start: 0.9229 (mmmt) cc_final: 0.8876 (mmtt) REVERT: G 266 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8234 (tt0) REVERT: G 317 PHE cc_start: 0.7921 (t80) cc_final: 0.7606 (m-80) outliers start: 108 outliers final: 58 residues processed: 329 average time/residue: 1.1060 time to fit residues: 414.8356 Evaluate side-chains 312 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 237 time to evaluate : 2.093 ------------------------------------------------------------------------------- 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 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 352 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 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 352 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 124 ASN Chi-restraints excluded: chain D residue 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 317 PHE Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 124 ASN Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 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 202 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 0.9980 chunk 108 optimal weight: 10.0000 chunk 185 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 111 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 G 355 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.126523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.084637 restraints weight = 30603.271| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.47 r_work: 0.2969 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18732 Z= 0.124 Angle : 0.625 11.062 25473 Z= 0.296 Chirality : 0.039 0.199 3045 Planarity : 0.003 0.032 3052 Dihedral : 4.616 55.112 2438 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 4.78 % Allowed : 24.48 % 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: 2.23 (0.19), residues: 2198 helix: 2.49 (0.14), residues: 1512 sheet: 0.32 (0.49), residues: 126 loop : -1.19 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 104 HIS 0.002 0.001 HIS F 106 PHE 0.010 0.001 PHE D 12 TYR 0.030 0.001 TYR E 232 ARG 0.008 0.001 ARG C 128 Details of bonding type rmsd hydrogen bonds : bond 0.03321 ( 1142) hydrogen bonds : angle 3.71105 ( 3363) SS BOND : bond 0.00221 ( 14) SS BOND : angle 1.45368 ( 28) covalent geometry : bond 0.00289 (18718) covalent geometry : angle 0.62381 (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 344 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 246 time to evaluate : 1.944 Fit side-chains REVERT: A 14 ASP cc_start: 0.8463 (m-30) cc_final: 0.7606 (p0) REVERT: A 144 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.8012 (mp0) REVERT: A 152 ARG cc_start: 0.6270 (ptm-80) cc_final: 0.5782 (mtm110) REVERT: A 240 PHE cc_start: 0.7639 (OUTLIER) cc_final: 0.7054 (m-80) REVERT: A 358 ASN cc_start: 0.8824 (t0) cc_final: 0.8461 (t0) REVERT: B 14 ASP cc_start: 0.8491 (m-30) cc_final: 0.7799 (p0) REVERT: B 144 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8026 (mp0) REVERT: B 152 ARG cc_start: 0.6283 (ptm-80) cc_final: 0.5765 (mtm110) REVERT: B 203 LYS cc_start: 0.9139 (mmmt) cc_final: 0.8790 (mmtt) REVERT: B 240 PHE cc_start: 0.7624 (OUTLIER) cc_final: 0.7384 (m-80) REVERT: B 266 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: B 306 ASN cc_start: 0.7549 (t0) cc_final: 0.7270 (t0) REVERT: B 317 PHE cc_start: 0.7832 (t80) cc_final: 0.7478 (m-80) REVERT: B 358 ASN cc_start: 0.8872 (t0) cc_final: 0.8513 (t0) REVERT: C 14 ASP cc_start: 0.8449 (m-30) cc_final: 0.7636 (p0) REVERT: C 144 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7986 (mp0) REVERT: C 152 ARG cc_start: 0.6100 (ptm-80) cc_final: 0.5622 (mtm110) REVERT: C 297 MET cc_start: 0.8169 (pmm) cc_final: 0.7885 (pmt) REVERT: C 306 ASN cc_start: 0.7619 (t0) cc_final: 0.7340 (t0) REVERT: C 352 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8611 (t) REVERT: D 14 ASP cc_start: 0.8283 (m-30) cc_final: 0.7598 (p0) REVERT: D 152 ARG cc_start: 0.6357 (ptm-80) cc_final: 0.5833 (mtm110) REVERT: D 200 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8382 (mm-40) REVERT: D 240 PHE cc_start: 0.7723 (OUTLIER) cc_final: 0.6423 (t80) REVERT: D 266 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8346 (tt0) REVERT: D 306 ASN cc_start: 0.7649 (t0) cc_final: 0.7339 (t0) REVERT: D 317 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7582 (m-80) REVERT: E 14 ASP cc_start: 0.8440 (m-30) cc_final: 0.7772 (p0) REVERT: E 144 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7965 (mp0) REVERT: E 152 ARG cc_start: 0.6231 (ptm-80) cc_final: 0.5730 (mtm110) REVERT: E 203 LYS cc_start: 0.9208 (mmmt) cc_final: 0.8894 (mptt) REVERT: E 266 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8095 (tt0) REVERT: E 306 ASN cc_start: 0.7569 (t0) cc_final: 0.7295 (t0) REVERT: F 14 ASP cc_start: 0.8520 (m-30) cc_final: 0.8002 (t0) REVERT: F 144 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8240 (mp0) REVERT: F 152 ARG cc_start: 0.6181 (ptm-80) cc_final: 0.5947 (ptm-80) REVERT: F 203 LYS cc_start: 0.9214 (mmmt) cc_final: 0.8883 (mptt) REVERT: F 266 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8240 (tt0) REVERT: F 280 TYR cc_start: 0.8138 (t80) cc_final: 0.7609 (m-80) REVERT: F 306 ASN cc_start: 0.7608 (t0) cc_final: 0.7354 (t0) REVERT: F 358 ASN cc_start: 0.8999 (t0) cc_final: 0.8695 (t0) REVERT: G 14 ASP cc_start: 0.8427 (m-30) cc_final: 0.7727 (p0) REVERT: G 128 ARG cc_start: 0.8592 (tmm-80) cc_final: 0.8364 (ttt-90) REVERT: G 144 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: G 152 ARG cc_start: 0.6238 (ptm-80) cc_final: 0.5724 (mtm110) REVERT: G 203 LYS cc_start: 0.9280 (mmmt) cc_final: 0.8912 (mmtt) REVERT: G 266 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8235 (tt0) REVERT: G 317 PHE cc_start: 0.7917 (t80) cc_final: 0.7608 (m-80) outliers start: 98 outliers final: 61 residues processed: 321 average time/residue: 1.0702 time to fit residues: 391.3927 Evaluate side-chains 313 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 237 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 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 266 GLN Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain D residue 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 317 PHE Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 124 ASN Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 124 ASN Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 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 266 GLN Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 352 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 121 optimal weight: 6.9990 chunk 223 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 182 optimal weight: 2.9990 chunk 65 optimal weight: 0.0270 chunk 118 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 222 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 155 optimal weight: 10.0000 overall best weight: 2.6044 ------------------------------------------------------------------------------- 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 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 355 ASN F 282 ASN F 355 ASN 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 = 0.3783 r_free = 0.3783 target = 0.125012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.082637 restraints weight = 30802.998| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.49 r_work: 0.2928 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18732 Z= 0.179 Angle : 0.663 12.302 25473 Z= 0.316 Chirality : 0.041 0.211 3045 Planarity : 0.003 0.040 3052 Dihedral : 4.779 59.406 2438 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 4.78 % Allowed : 24.62 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.07 (0.19), residues: 2198 helix: 2.34 (0.14), residues: 1519 sheet: 0.40 (0.49), residues: 126 loop : -1.25 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 127 HIS 0.004 0.001 HIS A 106 PHE 0.009 0.001 PHE D 12 TYR 0.036 0.002 TYR F 232 ARG 0.007 0.001 ARG D 29 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 1142) hydrogen bonds : angle 3.83002 ( 3363) SS BOND : bond 0.00141 ( 14) SS BOND : angle 1.52728 ( 28) covalent geometry : bond 0.00436 (18718) covalent geometry : angle 0.66179 (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 337 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 239 time to evaluate : 2.023 Fit side-chains REVERT: A 14 ASP cc_start: 0.8485 (m-30) cc_final: 0.7627 (p0) REVERT: A 144 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8061 (mp0) REVERT: A 152 ARG cc_start: 0.6231 (ptm-80) cc_final: 0.5716 (mtm110) REVERT: A 240 PHE cc_start: 0.7746 (OUTLIER) cc_final: 0.7214 (m-80) REVERT: A 358 ASN cc_start: 0.8833 (t0) cc_final: 0.8476 (t0) REVERT: B 14 ASP cc_start: 0.8517 (m-30) cc_final: 0.7818 (p0) REVERT: B 144 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8029 (mp0) REVERT: B 152 ARG cc_start: 0.6265 (ptm-80) cc_final: 0.5780 (mtm110) REVERT: B 203 LYS cc_start: 0.9181 (mmmt) cc_final: 0.8815 (mmtt) REVERT: B 240 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.7430 (m-80) REVERT: B 266 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8224 (tt0) REVERT: B 306 ASN cc_start: 0.7513 (t0) cc_final: 0.7245 (t0) REVERT: B 317 PHE cc_start: 0.7877 (t80) cc_final: 0.7522 (m-80) REVERT: B 358 ASN cc_start: 0.8887 (t0) cc_final: 0.8525 (t0) REVERT: C 14 ASP cc_start: 0.8491 (m-30) cc_final: 0.7756 (p0) REVERT: C 144 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7986 (mp0) REVERT: C 152 ARG cc_start: 0.6099 (ptm-80) cc_final: 0.5626 (mtm110) REVERT: C 200 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8377 (mm-40) REVERT: C 297 MET cc_start: 0.8210 (pmm) cc_final: 0.7966 (pmt) REVERT: C 306 ASN cc_start: 0.7677 (t0) cc_final: 0.7405 (t0) REVERT: D 14 ASP cc_start: 0.8343 (m-30) cc_final: 0.7612 (p0) REVERT: D 152 ARG cc_start: 0.6223 (ptm-80) cc_final: 0.5745 (mtm110) REVERT: D 240 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.6380 (t80) REVERT: D 266 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8291 (tp-100) REVERT: D 306 ASN cc_start: 0.7654 (t0) cc_final: 0.7353 (t0) REVERT: D 317 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7504 (m-80) REVERT: E 14 ASP cc_start: 0.8457 (m-30) cc_final: 0.7786 (p0) REVERT: E 144 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7968 (mp0) REVERT: E 152 ARG cc_start: 0.6205 (ptm-80) cc_final: 0.5715 (mtm110) REVERT: E 203 LYS cc_start: 0.9222 (mmmt) cc_final: 0.8910 (mptt) REVERT: E 266 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8173 (tt0) REVERT: E 306 ASN cc_start: 0.7591 (t0) cc_final: 0.7291 (t0) REVERT: F 14 ASP cc_start: 0.8553 (m-30) cc_final: 0.8017 (t0) REVERT: F 152 ARG cc_start: 0.6181 (ptm-80) cc_final: 0.5948 (ptm-80) REVERT: F 203 LYS cc_start: 0.9244 (mmmt) cc_final: 0.8907 (mptt) REVERT: F 266 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8302 (tt0) REVERT: F 280 TYR cc_start: 0.8150 (t80) cc_final: 0.7618 (m-80) REVERT: F 306 ASN cc_start: 0.7614 (t0) cc_final: 0.7357 (t0) REVERT: F 358 ASN cc_start: 0.9051 (t0) cc_final: 0.8760 (t0) REVERT: G 14 ASP cc_start: 0.8494 (m-30) cc_final: 0.7783 (p0) REVERT: G 144 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: G 152 ARG cc_start: 0.6228 (ptm-80) cc_final: 0.5719 (mtm110) REVERT: G 203 LYS cc_start: 0.9291 (mmmt) cc_final: 0.8925 (mmtt) REVERT: G 266 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8257 (tt0) REVERT: G 317 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7630 (m-80) outliers start: 98 outliers final: 63 residues processed: 315 average time/residue: 1.1106 time to fit residues: 398.2671 Evaluate side-chains 311 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 233 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 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 266 GLN Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain C residue 3 ILE 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 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 255 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 317 PHE Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 124 ASN Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 124 ASN Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 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 317 PHE 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: 0.9980 chunk 183 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 63 optimal weight: 7.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 340 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 = 0.3810 r_free = 0.3810 target = 0.127124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.085238 restraints weight = 30526.403| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.48 r_work: 0.2973 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2622 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= 0.123 Angle : 0.658 14.776 25473 Z= 0.312 Chirality : 0.040 0.202 3045 Planarity : 0.003 0.033 3052 Dihedral : 4.794 59.917 2438 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.90 % Allowed : 25.74 % Favored : 70.36 % 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: 2.24 (0.19), residues: 2198 helix: 2.48 (0.14), residues: 1512 sheet: 0.42 (0.49), residues: 126 loop : -1.14 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 74 HIS 0.002 0.001 HIS A 106 PHE 0.010 0.001 PHE C 12 TYR 0.028 0.001 TYR E 232 ARG 0.007 0.001 ARG D 29 Details of bonding type rmsd hydrogen bonds : bond 0.03258 ( 1142) hydrogen bonds : angle 3.75616 ( 3363) SS BOND : bond 0.00227 ( 14) SS BOND : angle 1.41553 ( 28) covalent geometry : bond 0.00283 (18718) covalent geometry : angle 0.65629 (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 328 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 248 time to evaluate : 2.105 Fit side-chains REVERT: A 14 ASP cc_start: 0.8471 (m-30) cc_final: 0.7554 (p0) REVERT: A 144 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: A 152 ARG cc_start: 0.6211 (ptm-80) cc_final: 0.5719 (mtm110) REVERT: A 240 PHE cc_start: 0.7638 (OUTLIER) cc_final: 0.7070 (m-80) REVERT: A 280 TYR cc_start: 0.8184 (t80) cc_final: 0.7590 (m-80) REVERT: A 358 ASN cc_start: 0.8840 (t0) cc_final: 0.8468 (t0) REVERT: B 14 ASP cc_start: 0.8441 (m-30) cc_final: 0.7827 (p0) REVERT: B 144 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: B 152 ARG cc_start: 0.6220 (ptm-80) cc_final: 0.5737 (mtm110) REVERT: B 203 LYS cc_start: 0.9148 (mmmt) cc_final: 0.8782 (mmtt) REVERT: B 240 PHE cc_start: 0.7624 (OUTLIER) cc_final: 0.7384 (m-80) REVERT: B 266 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8073 (tt0) REVERT: B 306 ASN cc_start: 0.7549 (t0) cc_final: 0.7274 (t0) REVERT: B 317 PHE cc_start: 0.7843 (t80) cc_final: 0.7518 (m-80) REVERT: B 358 ASN cc_start: 0.8931 (t0) cc_final: 0.8529 (t0) REVERT: B 374 THR cc_start: 0.8643 (p) cc_final: 0.8394 (t) REVERT: C 14 ASP cc_start: 0.8455 (m-30) cc_final: 0.7655 (p0) REVERT: C 144 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.8002 (mp0) REVERT: C 152 ARG cc_start: 0.6072 (ptm-80) cc_final: 0.5598 (mtm110) REVERT: C 200 GLN cc_start: 0.8593 (mm-40) cc_final: 0.8368 (mm-40) REVERT: C 297 MET cc_start: 0.8212 (pmm) cc_final: 0.7920 (pmt) REVERT: C 306 ASN cc_start: 0.7665 (t0) cc_final: 0.7391 (t0) REVERT: D 14 ASP cc_start: 0.8307 (m-30) cc_final: 0.7598 (p0) REVERT: D 152 ARG cc_start: 0.6293 (ptm-80) cc_final: 0.5766 (mtm110) REVERT: D 240 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.6298 (t80) REVERT: D 306 ASN cc_start: 0.7652 (t0) cc_final: 0.7386 (t0) REVERT: D 317 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7390 (m-80) REVERT: E 14 ASP cc_start: 0.8423 (m-30) cc_final: 0.7754 (p0) REVERT: E 144 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8023 (mp0) REVERT: E 152 ARG cc_start: 0.6192 (ptm-80) cc_final: 0.5704 (mtm110) REVERT: E 200 GLN cc_start: 0.8677 (mm-40) cc_final: 0.8425 (mm-40) REVERT: E 203 LYS cc_start: 0.9208 (mmmt) cc_final: 0.8903 (mptt) REVERT: E 280 TYR cc_start: 0.8279 (t80) cc_final: 0.7848 (m-80) REVERT: E 306 ASN cc_start: 0.7575 (t0) cc_final: 0.7293 (t0) REVERT: F 14 ASP cc_start: 0.8517 (m-30) cc_final: 0.7980 (t0) REVERT: F 152 ARG cc_start: 0.6151 (ptm-80) cc_final: 0.5901 (ptm-80) REVERT: F 203 LYS cc_start: 0.9201 (mmmt) cc_final: 0.8876 (mptt) REVERT: F 280 TYR cc_start: 0.8122 (t80) cc_final: 0.7586 (m-80) REVERT: F 306 ASN cc_start: 0.7634 (t0) cc_final: 0.7385 (t0) REVERT: F 358 ASN cc_start: 0.9052 (t0) cc_final: 0.8747 (t0) REVERT: G 14 ASP cc_start: 0.8450 (m-30) cc_final: 0.7742 (p0) REVERT: G 144 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7892 (mp0) REVERT: G 152 ARG cc_start: 0.6170 (ptm-80) cc_final: 0.5704 (mtm110) REVERT: G 203 LYS cc_start: 0.9247 (mmmt) cc_final: 0.8853 (mmtt) REVERT: G 266 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8263 (tt0) REVERT: G 317 PHE cc_start: 0.7908 (t80) cc_final: 0.7605 (m-80) outliers start: 80 outliers final: 55 residues processed: 311 average time/residue: 1.1916 time to fit residues: 426.5477 Evaluate side-chains 305 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 239 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 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 266 GLN 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 D residue 317 PHE Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 124 ASN Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 78 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 chunk 199 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 167 optimal weight: 3.9990 chunk 217 optimal weight: 5.9990 chunk 204 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.126594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.084588 restraints weight = 30549.877| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.48 r_work: 0.2963 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18732 Z= 0.135 Angle : 0.671 14.468 25473 Z= 0.318 Chirality : 0.040 0.208 3045 Planarity : 0.003 0.040 3052 Dihedral : 4.730 57.931 2438 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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: 2.18 (0.19), residues: 2198 helix: 2.41 (0.14), residues: 1519 sheet: 0.47 (0.49), residues: 126 loop : -1.16 (0.29), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 127 HIS 0.002 0.001 HIS B 106 PHE 0.009 0.001 PHE D 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 0.03342 ( 1142) hydrogen bonds : angle 3.78509 ( 3363) SS BOND : bond 0.00214 ( 14) SS BOND : angle 1.46080 ( 28) covalent geometry : bond 0.00318 (18718) covalent geometry : angle 0.66973 (25445) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11677.91 seconds wall clock time: 201 minutes 54.17 seconds (12114.17 seconds total)