Starting phenix.real_space_refine on Wed Jan 22 05:13:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bz8_45056/01_2025/9bz8_45056.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bz8_45056/01_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_45056/01_2025/9bz8_45056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bz8_45056/01_2025/9bz8_45056.map" model { file = "/net/cci-nas-00/data/ceres_data/9bz8_45056/01_2025/9bz8_45056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bz8_45056/01_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-5571/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: 6.27, 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=2, 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 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: 4.40 Conformation dependent library (CDL) restraints added in 2.5 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: 1.68 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: 5.47 Time building geometry restraints manager: 5.21 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: 9591 16.87 - 33.74: 1082 33.74 - 50.61: 378 50.61 - 67.48: 35 67.48 - 84.36: 22 Dihedral angle restraints: 11108 sinusoidal: 4367 harmonic: 6741 Sorted by residual: dihedral pdb=" CB CYS A 84 " pdb=" SG CYS A 84 " pdb=" SG CYS A 248 " pdb=" CB CYS A 248 " ideal model delta sinusoidal sigma weight residual 93.00 15.39 77.61 1 1.00e+01 1.00e-02 7.54e+01 dihedral pdb=" CA ASP E 364 " pdb=" CB ASP E 364 " pdb=" CG ASP E 364 " pdb=" OD1 ASP E 364 " ideal model delta sinusoidal sigma weight residual -30.00 -89.73 59.73 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA ASP C 364 " pdb=" CB ASP C 364 " pdb=" CG ASP C 364 " pdb=" OD1 ASP C 364 " ideal model delta sinusoidal sigma weight residual -30.00 -89.71 59.71 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 11105 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: 2.03 - 2.60: 121 2.60 - 3.18: 15335 3.18 - 3.75: 29563 3.75 - 4.33: 37205 4.33 - 4.90: 65176 Nonbonded interactions: 147400 Sorted by model distance: nonbonded pdb=" SG CYS B 84 " pdb=" SG CYS B 248 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS E 84 " pdb=" SG CYS E 248 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS D 84 " pdb=" SG CYS D 248 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS C 84 " pdb=" SG CYS C 248 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS G 84 " pdb=" SG CYS G 248 " model vdw 2.030 3.760 ... (remaining 147395 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: 0.12 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 35.130 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.980 ------------------------------------------------------------------------------- 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 18718 Z= 0.140 Angle : 0.512 6.613 25445 Z= 0.259 Chirality : 0.038 0.258 3045 Planarity : 0.003 0.029 3052 Dihedral : 16.193 84.356 6720 Min Nonbonded Distance : 2.029 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 *********************** 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 : 2.205 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: 1.4052 time to fit residues: 649.9510 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 : 2.070 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.124592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.082071 restraints weight = 31089.026| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.46 r_work: 0.2917 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 18718 Z= 0.384 Angle : 0.654 8.069 25445 Z= 0.321 Chirality : 0.042 0.215 3045 Planarity : 0.004 0.033 3052 Dihedral : 4.527 48.643 2451 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 6.58 % Allowed : 23.84 % Favored : 69.58 % 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: 1.99 (0.19), residues: 2198 helix: 2.33 (0.13), residues: 1526 sheet: 0.05 (0.48), residues: 126 loop : -1.41 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 127 HIS 0.005 0.001 HIS B 106 PHE 0.017 0.002 PHE B 333 TYR 0.024 0.002 TYR A 232 ARG 0.005 0.001 ARG B 128 *********************** 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 392 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 257 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8461 (m-30) cc_final: 0.7980 (t0) REVERT: A 124 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7900 (p0) REVERT: A 144 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.8043 (mp0) REVERT: A 152 ARG cc_start: 0.6231 (ptm-80) cc_final: 0.5800 (mtm110) REVERT: A 240 PHE cc_start: 0.7572 (OUTLIER) cc_final: 0.7047 (m-80) REVERT: A 358 ASN cc_start: 0.8787 (t0) cc_final: 0.8439 (t0) REVERT: B 14 ASP cc_start: 0.8661 (m-30) cc_final: 0.7825 (p0) REVERT: B 144 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8091 (mp0) REVERT: B 152 ARG cc_start: 0.6177 (ptm-80) cc_final: 0.5756 (mtm110) REVERT: B 240 PHE cc_start: 0.7658 (OUTLIER) cc_final: 0.7341 (m-80) REVERT: B 358 ASN cc_start: 0.8810 (t0) cc_final: 0.8416 (t0) REVERT: C 14 ASP cc_start: 0.8604 (m-30) cc_final: 0.7747 (p0) REVERT: C 152 ARG cc_start: 0.6071 (ptm-80) cc_final: 0.5739 (mtm110) REVERT: C 297 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7524 (pmm) REVERT: D 124 ASN cc_start: 0.8204 (OUTLIER) cc_final: 0.7920 (p0) REVERT: D 152 ARG cc_start: 0.6185 (ptm-80) cc_final: 0.5760 (mtm110) REVERT: D 306 ASN cc_start: 0.7685 (t0) cc_final: 0.7438 (t0) REVERT: E 14 ASP cc_start: 0.8591 (m-30) cc_final: 0.7868 (p0) REVERT: E 144 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: E 152 ARG cc_start: 0.6220 (ptm-80) cc_final: 0.5770 (mtm110) REVERT: E 200 GLN cc_start: 0.8869 (mm-40) cc_final: 0.8306 (mm-40) REVERT: E 297 MET cc_start: 0.7861 (pmm) cc_final: 0.7592 (pmm) REVERT: E 306 ASN cc_start: 0.7541 (t0) cc_final: 0.7060 (t0) REVERT: F 14 ASP cc_start: 0.8552 (m-30) cc_final: 0.7899 (t70) REVERT: F 152 ARG cc_start: 0.6236 (ptm-80) cc_final: 0.5970 (mtp-110) REVERT: F 358 ASN cc_start: 0.8860 (t0) cc_final: 0.8580 (t0) REVERT: G 14 ASP cc_start: 0.8603 (m-30) cc_final: 0.7869 (p0) REVERT: G 144 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7930 (mp0) REVERT: G 152 ARG cc_start: 0.6131 (ptm-80) cc_final: 0.5669 (mtm110) REVERT: G 317 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.7590 (m-80) outliers start: 135 outliers final: 47 residues processed: 363 average time/residue: 1.2245 time to fit residues: 502.0790 Evaluate side-chains 302 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 245 time to evaluate : 2.123 ------------------------------------------------------------------------------- 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 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 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 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 255 LEU Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain G residue 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 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: 9.9990 chunk 55 optimal weight: 0.8980 chunk 110 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 ASN C 266 GLN C 355 ASN D 355 ASN E 355 ASN F 355 ASN G 5 HIS 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 = 0.3781 r_free = 0.3781 target = 0.124791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.082228 restraints weight = 30706.831| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.46 r_work: 0.2925 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18718 Z= 0.251 Angle : 0.598 8.078 25445 Z= 0.289 Chirality : 0.040 0.182 3045 Planarity : 0.003 0.029 3052 Dihedral : 4.332 51.724 2440 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 6.09 % Allowed : 23.26 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.04 (0.19), residues: 2198 helix: 2.36 (0.13), residues: 1526 sheet: 0.25 (0.48), residues: 126 loop : -1.42 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 85 HIS 0.003 0.001 HIS B 106 PHE 0.010 0.001 PHE D 240 TYR 0.022 0.002 TYR E 232 ARG 0.005 0.001 ARG F 29 *********************** 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 374 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 249 time to evaluate : 1.981 Fit side-chains revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8435 (m-30) cc_final: 0.7996 (t0) REVERT: A 124 ASN cc_start: 0.8138 (OUTLIER) cc_final: 0.7853 (p0) REVERT: A 144 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7995 (mp0) REVERT: A 152 ARG cc_start: 0.6295 (ptm-80) cc_final: 0.5803 (mtm110) REVERT: A 240 PHE cc_start: 0.7702 (OUTLIER) cc_final: 0.7151 (m-80) REVERT: A 358 ASN cc_start: 0.8802 (t0) cc_final: 0.8458 (t0) REVERT: B 14 ASP cc_start: 0.8604 (m-30) cc_final: 0.7819 (p0) REVERT: B 144 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8014 (mp0) REVERT: B 152 ARG cc_start: 0.6239 (ptm-80) cc_final: 0.5741 (mtm110) REVERT: B 240 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.7376 (m-80) REVERT: B 266 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8243 (tt0) REVERT: B 306 ASN cc_start: 0.7534 (t0) cc_final: 0.7036 (t0) REVERT: B 309 LYS cc_start: 0.9084 (mmtt) cc_final: 0.8865 (mmtp) REVERT: B 358 ASN cc_start: 0.8833 (t0) cc_final: 0.8449 (t0) REVERT: C 14 ASP cc_start: 0.8462 (m-30) cc_final: 0.7701 (p0) REVERT: C 152 ARG cc_start: 0.6123 (ptm-80) cc_final: 0.5746 (mtm110) REVERT: D 14 ASP cc_start: 0.8290 (m-30) cc_final: 0.7593 (p0) REVERT: D 124 ASN cc_start: 0.8254 (OUTLIER) cc_final: 0.7975 (p0) REVERT: D 152 ARG cc_start: 0.6203 (ptm-80) cc_final: 0.5707 (mtm110) REVERT: D 290 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8639 (mmm) REVERT: D 306 ASN cc_start: 0.7582 (t0) cc_final: 0.7319 (t0) REVERT: E 14 ASP cc_start: 0.8505 (m-30) cc_final: 0.7787 (p0) REVERT: E 144 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7920 (mp0) REVERT: E 152 ARG cc_start: 0.6210 (ptm-80) cc_final: 0.5752 (mtm110) REVERT: E 266 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8438 (tt0) REVERT: E 297 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7714 (pmm) REVERT: E 306 ASN cc_start: 0.7553 (t0) cc_final: 0.7286 (t0) REVERT: F 14 ASP cc_start: 0.8573 (m-30) cc_final: 0.7864 (t0) REVERT: F 124 ASN cc_start: 0.8136 (OUTLIER) cc_final: 0.7828 (p0) REVERT: F 152 ARG cc_start: 0.6210 (ptm-80) cc_final: 0.5861 (mtm110) REVERT: F 358 ASN cc_start: 0.8866 (t0) cc_final: 0.8585 (t0) REVERT: G 14 ASP cc_start: 0.8522 (m-30) cc_final: 0.7824 (p0) REVERT: G 29 ARG cc_start: 0.8883 (mtm-85) cc_final: 0.8615 (mtt180) REVERT: G 128 ARG cc_start: 0.8649 (tmm-80) cc_final: 0.8390 (ttt-90) REVERT: G 144 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7839 (mp0) REVERT: G 152 ARG cc_start: 0.6259 (ptm-80) cc_final: 0.5728 (mtm110) REVERT: G 266 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8416 (tt0) REVERT: G 317 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7584 (m-80) outliers start: 125 outliers final: 52 residues processed: 347 average time/residue: 1.0926 time to fit residues: 435.8256 Evaluate side-chains 307 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 240 time to evaluate : 1.805 ------------------------------------------------------------------------------- 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 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 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 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 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 287 VAL Chi-restraints excluded: chain D residue 290 MET 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 297 MET Chi-restraints excluded: chain E residue 341 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 30 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 163 optimal weight: 10.0000 chunk 62 optimal weight: 0.0170 chunk 133 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN B 355 ASN C 266 GLN C 340 ASN C 355 ASN D 340 ASN D 355 ASN E 340 ASN E 355 ASN F 340 ASN F 355 ASN G 56 GLN G 355 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.125938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.083666 restraints weight = 30526.278| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.46 r_work: 0.2949 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18718 Z= 0.184 Angle : 0.593 8.748 25445 Z= 0.282 Chirality : 0.039 0.178 3045 Planarity : 0.003 0.028 3052 Dihedral : 4.341 52.944 2439 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 5.12 % Allowed : 24.28 % 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: 2.19 (0.19), residues: 2198 helix: 2.48 (0.13), residues: 1519 sheet: 0.26 (0.48), residues: 126 loop : -1.30 (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 0.010 0.001 PHE D 12 TYR 0.023 0.001 TYR E 232 ARG 0.006 0.001 ARG F 29 *********************** 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 354 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 249 time to evaluate : 1.621 Fit side-chains revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8454 (m-30) cc_final: 0.7983 (t0) REVERT: A 124 ASN cc_start: 0.8083 (OUTLIER) cc_final: 0.7729 (p0) REVERT: A 144 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8035 (mp0) REVERT: A 152 ARG cc_start: 0.6301 (ptm-80) cc_final: 0.5796 (mtm110) REVERT: A 240 PHE cc_start: 0.7661 (OUTLIER) cc_final: 0.7129 (m-80) REVERT: A 358 ASN cc_start: 0.8809 (t0) cc_final: 0.8464 (t0) REVERT: B 14 ASP cc_start: 0.8576 (m-30) cc_final: 0.7821 (p0) REVERT: B 144 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7993 (mp0) REVERT: B 152 ARG cc_start: 0.6191 (ptm-80) cc_final: 0.5739 (mtm110) REVERT: B 203 LYS cc_start: 0.9195 (mmmt) cc_final: 0.8772 (mmtt) REVERT: B 240 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.7323 (m-80) REVERT: B 266 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8201 (tt0) REVERT: B 306 ASN cc_start: 0.7501 (t0) cc_final: 0.6952 (t0) REVERT: B 309 LYS cc_start: 0.9078 (mmtt) cc_final: 0.8867 (mmtp) REVERT: B 358 ASN cc_start: 0.8844 (t0) cc_final: 0.8443 (t0) REVERT: C 14 ASP cc_start: 0.8468 (m-30) cc_final: 0.7709 (p0) REVERT: C 152 ARG cc_start: 0.6126 (ptm-80) cc_final: 0.5689 (mtm110) REVERT: C 297 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7811 (pmt) REVERT: C 306 ASN cc_start: 0.7293 (t0) cc_final: 0.7032 (t0) REVERT: C 352 VAL cc_start: 0.8732 (OUTLIER) cc_final: 0.8504 (t) REVERT: D 14 ASP cc_start: 0.8286 (m-30) cc_final: 0.7582 (p0) REVERT: D 124 ASN cc_start: 0.8285 (OUTLIER) cc_final: 0.7995 (p0) REVERT: D 152 ARG cc_start: 0.6196 (ptm-80) cc_final: 0.5711 (mtm110) REVERT: D 240 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.6310 (t80) REVERT: D 266 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8405 (tp-100) REVERT: D 306 ASN cc_start: 0.7575 (t0) cc_final: 0.7300 (t0) REVERT: D 317 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.7631 (m-80) REVERT: E 14 ASP cc_start: 0.8494 (m-30) cc_final: 0.7802 (p0) REVERT: E 144 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7917 (mp0) REVERT: E 152 ARG cc_start: 0.6251 (ptm-80) cc_final: 0.5804 (mtm110) REVERT: E 203 LYS cc_start: 0.9260 (mmmt) cc_final: 0.8845 (mmtt) REVERT: E 266 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8387 (tt0) REVERT: E 297 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7695 (pmm) REVERT: E 306 ASN cc_start: 0.7556 (t0) cc_final: 0.7302 (t0) REVERT: F 14 ASP cc_start: 0.8561 (m-30) cc_final: 0.7870 (t0) REVERT: F 124 ASN cc_start: 0.8139 (OUTLIER) cc_final: 0.7815 (p0) REVERT: F 152 ARG cc_start: 0.6202 (ptm-80) cc_final: 0.5820 (mtm110) REVERT: F 203 LYS cc_start: 0.9190 (mmmt) cc_final: 0.8838 (mptt) REVERT: F 266 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8187 (tt0) REVERT: F 358 ASN cc_start: 0.8877 (t0) cc_final: 0.8602 (t0) REVERT: G 14 ASP cc_start: 0.8483 (m-30) cc_final: 0.7716 (p0) REVERT: G 29 ARG cc_start: 0.8883 (mtm-85) cc_final: 0.8610 (mtt180) REVERT: G 128 ARG cc_start: 0.8590 (tmm-80) cc_final: 0.8316 (ttt-90) REVERT: G 144 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: G 152 ARG cc_start: 0.6254 (ptm-80) cc_final: 0.5733 (mtm110) REVERT: G 266 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8422 (tt0) REVERT: G 317 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.7577 (m-80) outliers start: 105 outliers final: 46 residues processed: 326 average time/residue: 1.1444 time to fit residues: 424.3173 Evaluate side-chains 307 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 241 time to evaluate : 2.248 ------------------------------------------------------------------------------- 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 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 144 GLU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 124 ASN Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 266 GLN Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 276 ARG Chi-restraints excluded: chain D residue 290 MET 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 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 297 MET Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 124 ASN Chi-restraints excluded: chain F residue 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 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 317 PHE 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: 0.9990 chunk 194 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 184 optimal weight: 0.2980 chunk 218 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 174 optimal weight: 9.9990 chunk 152 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN B 355 ASN C 266 GLN C 340 ASN C 355 ASN D 355 ASN E 355 ASN F 282 ASN F 355 ASN G 56 GLN G 282 ASN G 355 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.124722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.082382 restraints weight = 30655.617| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.45 r_work: 0.2924 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 18718 Z= 0.238 Angle : 0.606 8.811 25445 Z= 0.289 Chirality : 0.040 0.189 3045 Planarity : 0.003 0.028 3052 Dihedral : 4.310 53.388 2437 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 6.00 % Allowed : 23.70 % Favored : 70.31 % 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: 2.11 (0.19), residues: 2198 helix: 2.38 (0.13), residues: 1519 sheet: 0.37 (0.49), residues: 126 loop : -1.25 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 85 HIS 0.004 0.001 HIS C 106 PHE 0.010 0.001 PHE B 129 TYR 0.028 0.001 TYR F 232 ARG 0.006 0.000 ARG F 29 *********************** 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 374 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 251 time to evaluate : 2.056 Fit side-chains REVERT: A 14 ASP cc_start: 0.8488 (m-30) cc_final: 0.7614 (p0) REVERT: A 124 ASN cc_start: 0.8164 (OUTLIER) cc_final: 0.7760 (p0) REVERT: A 144 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8010 (mp0) REVERT: A 152 ARG cc_start: 0.6306 (ptm-80) cc_final: 0.5809 (mtm110) REVERT: A 240 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7254 (m-80) REVERT: A 358 ASN cc_start: 0.8821 (t0) cc_final: 0.8473 (t0) REVERT: B 14 ASP cc_start: 0.8564 (m-30) cc_final: 0.7829 (p0) REVERT: B 144 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7964 (mp0) REVERT: B 152 ARG cc_start: 0.6279 (ptm-80) cc_final: 0.5821 (mtm110) REVERT: B 203 LYS cc_start: 0.9181 (mmmt) cc_final: 0.8774 (mmtt) REVERT: B 240 PHE cc_start: 0.7689 (OUTLIER) cc_final: 0.7429 (m-80) REVERT: B 266 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8337 (tt0) REVERT: B 306 ASN cc_start: 0.7542 (t0) cc_final: 0.6984 (t0) REVERT: B 309 LYS cc_start: 0.9067 (mmtt) cc_final: 0.8861 (mmtp) REVERT: B 358 ASN cc_start: 0.8873 (t0) cc_final: 0.8475 (t0) REVERT: C 14 ASP cc_start: 0.8467 (m-30) cc_final: 0.7693 (p0) REVERT: C 144 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7989 (mp0) REVERT: C 152 ARG cc_start: 0.6096 (ptm-80) cc_final: 0.5657 (mtm110) REVERT: C 297 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7983 (pmt) REVERT: C 306 ASN cc_start: 0.7511 (t0) cc_final: 0.7258 (t0) REVERT: D 14 ASP cc_start: 0.8300 (m-30) cc_final: 0.7583 (p0) REVERT: D 124 ASN cc_start: 0.8327 (OUTLIER) cc_final: 0.7977 (p0) REVERT: D 152 ARG cc_start: 0.6278 (ptm-80) cc_final: 0.5793 (mtm110) REVERT: D 240 PHE cc_start: 0.7747 (OUTLIER) cc_final: 0.6347 (t80) REVERT: D 266 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8411 (tp-100) REVERT: D 306 ASN cc_start: 0.7615 (t0) cc_final: 0.7321 (t0) REVERT: D 317 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7608 (m-80) REVERT: E 14 ASP cc_start: 0.8492 (m-30) cc_final: 0.7804 (p0) REVERT: E 144 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7932 (mp0) REVERT: E 152 ARG cc_start: 0.6219 (ptm-80) cc_final: 0.5766 (mtm110) REVERT: E 200 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8560 (mm-40) REVERT: E 203 LYS cc_start: 0.9274 (mmmt) cc_final: 0.8838 (mmtt) REVERT: E 266 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8444 (tt0) REVERT: E 297 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7587 (pmm) REVERT: E 306 ASN cc_start: 0.7595 (t0) cc_final: 0.7319 (t0) REVERT: F 14 ASP cc_start: 0.8577 (m-30) cc_final: 0.7869 (t0) REVERT: F 152 ARG cc_start: 0.6212 (ptm-80) cc_final: 0.5833 (mtm110) REVERT: F 203 LYS cc_start: 0.9234 (mmmt) cc_final: 0.8880 (mptt) REVERT: F 266 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8241 (tt0) REVERT: F 358 ASN cc_start: 0.8926 (t0) cc_final: 0.8655 (t0) REVERT: G 14 ASP cc_start: 0.8478 (m-30) cc_final: 0.7711 (p0) REVERT: G 29 ARG cc_start: 0.8840 (mtm-85) cc_final: 0.8536 (mtt180) REVERT: G 128 ARG cc_start: 0.8659 (tmm-80) cc_final: 0.8368 (ttt180) REVERT: G 144 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: G 152 ARG cc_start: 0.6254 (ptm-80) cc_final: 0.5729 (mtm110) REVERT: G 203 LYS cc_start: 0.9255 (mmmt) cc_final: 0.8849 (mmtt) REVERT: G 266 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8464 (tt0) REVERT: G 317 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.7614 (m-80) outliers start: 123 outliers final: 56 residues processed: 345 average time/residue: 1.1184 time to fit residues: 440.3215 Evaluate side-chains 319 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 244 time to evaluate : 2.121 ------------------------------------------------------------------------------- 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 3 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 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 341 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 290 MET 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 240 PHE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 124 ASN Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 266 GLN Chi-restraints excluded: chain F residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 163 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 221 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 210 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 56 GLN B 340 ASN B 355 ASN C 266 GLN C 282 ASN C 340 ASN C 355 ASN D 355 ASN E 355 ASN F 266 GLN F 282 ASN F 340 ASN G 56 GLN G 355 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.124318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.081527 restraints weight = 30714.473| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.48 r_work: 0.2912 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18718 Z= 0.260 Angle : 0.621 8.375 25445 Z= 0.297 Chirality : 0.040 0.197 3045 Planarity : 0.003 0.030 3052 Dihedral : 4.266 54.051 2434 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 5.75 % Allowed : 23.79 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.04 (0.19), residues: 2198 helix: 2.36 (0.13), residues: 1512 sheet: 0.34 (0.49), residues: 126 loop : -1.33 (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 A 106 PHE 0.010 0.001 PHE A 333 TYR 0.029 0.002 TYR E 232 ARG 0.007 0.001 ARG D 29 *********************** 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 368 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 250 time to evaluate : 2.180 Fit side-chains REVERT: A 14 ASP cc_start: 0.8470 (m-30) cc_final: 0.7609 (p0) REVERT: A 124 ASN cc_start: 0.8267 (OUTLIER) cc_final: 0.7813 (p0) REVERT: A 144 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8000 (mp0) REVERT: A 152 ARG cc_start: 0.6302 (ptm-80) cc_final: 0.5791 (mtm110) REVERT: A 240 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7339 (m-80) REVERT: A 317 PHE cc_start: 0.7911 (t80) cc_final: 0.7679 (m-80) REVERT: A 358 ASN cc_start: 0.8814 (t0) cc_final: 0.8455 (t0) REVERT: B 14 ASP cc_start: 0.8560 (m-30) cc_final: 0.7852 (p0) REVERT: B 144 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7976 (mp0) REVERT: B 152 ARG cc_start: 0.6289 (ptm-80) cc_final: 0.5825 (mtm110) REVERT: B 203 LYS cc_start: 0.9182 (mmmt) cc_final: 0.8761 (mmtt) REVERT: B 240 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.7475 (m-80) REVERT: B 266 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8364 (tt0) REVERT: B 306 ASN cc_start: 0.7580 (t0) cc_final: 0.7022 (t0) REVERT: B 309 LYS cc_start: 0.9074 (mmtt) cc_final: 0.8871 (mmtp) REVERT: B 317 PHE cc_start: 0.7861 (t80) cc_final: 0.7500 (m-80) REVERT: B 358 ASN cc_start: 0.8869 (t0) cc_final: 0.8472 (t0) REVERT: C 14 ASP cc_start: 0.8462 (m-30) cc_final: 0.7714 (p0) REVERT: C 144 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7989 (mp0) REVERT: C 152 ARG cc_start: 0.6119 (ptm-80) cc_final: 0.5659 (mtm110) REVERT: C 200 GLN cc_start: 0.8514 (mm-40) cc_final: 0.8279 (mm-40) REVERT: C 297 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7984 (pmt) REVERT: C 306 ASN cc_start: 0.7607 (t0) cc_final: 0.7342 (t0) REVERT: D 14 ASP cc_start: 0.8337 (m-30) cc_final: 0.7600 (p0) REVERT: D 124 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.7801 (p0) REVERT: D 152 ARG cc_start: 0.6216 (ptm-80) cc_final: 0.5745 (mtm110) REVERT: D 266 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8481 (tp-100) REVERT: D 306 ASN cc_start: 0.7646 (t0) cc_final: 0.7352 (t0) REVERT: D 317 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7594 (m-80) REVERT: E 14 ASP cc_start: 0.8456 (m-30) cc_final: 0.7757 (p0) REVERT: E 144 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7936 (mp0) REVERT: E 152 ARG cc_start: 0.6252 (ptm-80) cc_final: 0.5761 (mtm110) REVERT: E 203 LYS cc_start: 0.9258 (mmmt) cc_final: 0.8913 (mptt) REVERT: E 266 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8448 (tt0) REVERT: E 297 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7563 (pmm) REVERT: E 306 ASN cc_start: 0.7568 (t0) cc_final: 0.7270 (t0) REVERT: F 14 ASP cc_start: 0.8574 (m-30) cc_final: 0.8009 (t0) REVERT: F 144 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8262 (mp0) REVERT: F 152 ARG cc_start: 0.6239 (ptm-80) cc_final: 0.5845 (mtm110) REVERT: F 203 LYS cc_start: 0.9240 (mmmt) cc_final: 0.8901 (mptt) REVERT: F 280 TYR cc_start: 0.8177 (t80) cc_final: 0.7649 (m-80) REVERT: F 297 MET cc_start: 0.8114 (pmt) cc_final: 0.7881 (pmt) REVERT: F 358 ASN cc_start: 0.8973 (t0) cc_final: 0.8697 (t0) REVERT: G 14 ASP cc_start: 0.8488 (m-30) cc_final: 0.7723 (p0) REVERT: G 128 ARG cc_start: 0.8671 (tmm-80) cc_final: 0.8465 (ttt-90) REVERT: G 144 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7868 (mp0) REVERT: G 152 ARG cc_start: 0.6243 (ptm-80) cc_final: 0.5746 (mtm110) REVERT: G 203 LYS cc_start: 0.9248 (mmmt) cc_final: 0.8878 (mmtt) REVERT: G 266 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8474 (tt0) REVERT: G 317 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7634 (m-80) outliers start: 118 outliers final: 60 residues processed: 344 average time/residue: 1.1258 time to fit residues: 442.4567 Evaluate side-chains 320 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 243 time to evaluate : 2.235 ------------------------------------------------------------------------------- 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 144 GLU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 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 341 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 341 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 202 LEU Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 287 VAL Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 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 287 VAL Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 164 optimal weight: 0.9980 chunk 30 optimal weight: 20.0000 chunk 213 optimal weight: 0.0670 chunk 193 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 181 optimal weight: 0.0870 chunk 118 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- 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 340 ASN D 355 ASN E 340 ASN E 355 ASN F 340 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 = 0.3799 r_free = 0.3799 target = 0.126382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.084267 restraints weight = 30419.574| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.47 r_work: 0.2964 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18718 Z= 0.168 Angle : 0.604 12.382 25445 Z= 0.286 Chirality : 0.039 0.185 3045 Planarity : 0.003 0.030 3052 Dihedral : 4.308 55.287 2434 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.53 % Allowed : 25.35 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.19), residues: 2198 helix: 2.46 (0.13), residues: 1512 sheet: 0.34 (0.49), residues: 126 loop : -1.20 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 74 HIS 0.002 0.001 HIS E 106 PHE 0.010 0.001 PHE D 12 TYR 0.027 0.001 TYR E 232 ARG 0.007 0.001 ARG D 29 *********************** 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 353 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 260 time to evaluate : 2.340 Fit side-chains REVERT: A 14 ASP cc_start: 0.8449 (m-30) cc_final: 0.7510 (p0) REVERT: A 144 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8020 (mp0) REVERT: A 152 ARG cc_start: 0.6232 (ptm-80) cc_final: 0.5745 (mtm110) REVERT: A 203 LYS cc_start: 0.9257 (mmmt) cc_final: 0.8869 (mptt) REVERT: A 240 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.7143 (m-80) REVERT: A 280 TYR cc_start: 0.8211 (t80) cc_final: 0.7611 (m-80) REVERT: A 317 PHE cc_start: 0.7863 (t80) cc_final: 0.7655 (m-80) REVERT: A 358 ASN cc_start: 0.8826 (t0) cc_final: 0.8472 (t0) REVERT: B 14 ASP cc_start: 0.8492 (m-30) cc_final: 0.7811 (p0) REVERT: B 144 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: B 152 ARG cc_start: 0.6194 (ptm-80) cc_final: 0.5704 (mtm110) REVERT: B 203 LYS cc_start: 0.9147 (mmmt) cc_final: 0.8759 (mmtt) REVERT: B 240 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.7403 (m-80) REVERT: B 266 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8239 (tt0) REVERT: B 306 ASN cc_start: 0.7563 (t0) cc_final: 0.7004 (t0) REVERT: B 358 ASN cc_start: 0.8865 (t0) cc_final: 0.8503 (t0) REVERT: C 14 ASP cc_start: 0.8447 (m-30) cc_final: 0.7641 (p0) REVERT: C 144 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7968 (mp0) REVERT: C 152 ARG cc_start: 0.6107 (ptm-80) cc_final: 0.5656 (mtm110) REVERT: C 200 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8297 (mm-40) REVERT: C 306 ASN cc_start: 0.7647 (t0) cc_final: 0.7375 (t0) REVERT: C 352 VAL cc_start: 0.8795 (OUTLIER) cc_final: 0.8568 (t) REVERT: D 14 ASP cc_start: 0.8324 (m-30) cc_final: 0.7600 (p0) REVERT: D 152 ARG cc_start: 0.6298 (ptm-80) cc_final: 0.5774 (mtm110) REVERT: D 240 PHE cc_start: 0.7747 (OUTLIER) cc_final: 0.6375 (t80) REVERT: D 306 ASN cc_start: 0.7633 (t0) cc_final: 0.7341 (t0) REVERT: E 14 ASP cc_start: 0.8416 (m-30) cc_final: 0.7741 (p0) REVERT: E 144 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7966 (mp0) REVERT: E 152 ARG cc_start: 0.6235 (ptm-80) cc_final: 0.5761 (mtm110) REVERT: E 203 LYS cc_start: 0.9220 (mmmt) cc_final: 0.8910 (mptt) REVERT: E 266 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8421 (tt0) REVERT: E 297 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7595 (pmm) REVERT: E 306 ASN cc_start: 0.7555 (t0) cc_final: 0.7261 (t0) REVERT: F 14 ASP cc_start: 0.8532 (m-30) cc_final: 0.8006 (t0) REVERT: F 89 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7710 (tt0) REVERT: F 144 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8255 (mp0) REVERT: F 152 ARG cc_start: 0.6155 (ptm-80) cc_final: 0.5736 (mtm110) REVERT: F 203 LYS cc_start: 0.9205 (mmmt) cc_final: 0.8869 (mptt) REVERT: F 280 TYR cc_start: 0.8150 (t80) cc_final: 0.7623 (m-80) REVERT: F 358 ASN cc_start: 0.8987 (t0) cc_final: 0.8701 (t0) REVERT: G 14 ASP cc_start: 0.8465 (m-30) cc_final: 0.7753 (p0) REVERT: G 128 ARG cc_start: 0.8601 (tmm-80) cc_final: 0.8383 (ttt-90) REVERT: G 144 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7865 (mp0) REVERT: G 152 ARG cc_start: 0.6229 (ptm-80) cc_final: 0.5728 (mtm110) REVERT: G 203 LYS cc_start: 0.9217 (mmmt) cc_final: 0.8869 (mmtt) REVERT: G 266 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8438 (tt0) REVERT: G 317 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.7614 (m-80) outliers start: 93 outliers final: 51 residues processed: 327 average time/residue: 1.1971 time to fit residues: 444.6234 Evaluate side-chains 313 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 247 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain D residue 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 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 266 GLN Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 124 ASN Chi-restraints excluded: chain F residue 138 ASP Chi-restraints excluded: chain F residue 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 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 317 PHE 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: 0.5980 chunk 108 optimal weight: 1.9990 chunk 185 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 111 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN A 355 ASN B 56 GLN B 355 ASN C 266 GLN C 282 ASN C 340 ASN C 355 ASN D 355 ASN E 355 ASN F 340 ASN F 355 ASN G 56 GLN G 355 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.126127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.084117 restraints weight = 30513.887| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.47 r_work: 0.2963 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18718 Z= 0.181 Angle : 0.618 12.116 25445 Z= 0.292 Chirality : 0.039 0.197 3045 Planarity : 0.003 0.032 3052 Dihedral : 4.388 56.928 2434 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 4.34 % Allowed : 25.50 % Favored : 70.16 % 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: 2.22 (0.19), residues: 2198 helix: 2.48 (0.14), residues: 1512 sheet: 0.32 (0.49), residues: 126 loop : -1.16 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 104 HIS 0.002 0.001 HIS G 106 PHE 0.010 0.001 PHE D 12 TYR 0.030 0.001 TYR G 232 ARG 0.007 0.001 ARG F 29 *********************** 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 338 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 249 time to evaluate : 2.006 Fit side-chains REVERT: A 14 ASP cc_start: 0.8457 (m-30) cc_final: 0.7517 (p0) REVERT: A 144 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8005 (mp0) REVERT: A 152 ARG cc_start: 0.6252 (ptm-80) cc_final: 0.5731 (mtm110) REVERT: A 240 PHE cc_start: 0.7647 (OUTLIER) cc_final: 0.7074 (m-80) REVERT: A 280 TYR cc_start: 0.8225 (t80) cc_final: 0.7628 (m-80) REVERT: A 358 ASN cc_start: 0.8833 (t0) cc_final: 0.8475 (t0) REVERT: B 14 ASP cc_start: 0.8483 (m-30) cc_final: 0.7825 (p0) REVERT: B 144 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8010 (mp0) REVERT: B 152 ARG cc_start: 0.6295 (ptm-80) cc_final: 0.5799 (mtm110) REVERT: B 203 LYS cc_start: 0.9172 (mmmt) cc_final: 0.8809 (mmtt) REVERT: B 240 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.7393 (m-80) REVERT: B 266 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8402 (tp40) REVERT: B 306 ASN cc_start: 0.7603 (t0) cc_final: 0.7394 (t0) REVERT: B 358 ASN cc_start: 0.8873 (t0) cc_final: 0.8499 (t0) REVERT: C 14 ASP cc_start: 0.8440 (m-30) cc_final: 0.7646 (p0) REVERT: C 144 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.8022 (mp0) REVERT: C 152 ARG cc_start: 0.6122 (ptm-80) cc_final: 0.5662 (mtm110) REVERT: C 297 MET cc_start: 0.8215 (pmm) cc_final: 0.7994 (pmt) REVERT: C 306 ASN cc_start: 0.7658 (t0) cc_final: 0.7411 (t0) REVERT: D 14 ASP cc_start: 0.8334 (m-30) cc_final: 0.7612 (p0) REVERT: D 152 ARG cc_start: 0.6323 (ptm-80) cc_final: 0.5788 (mtm110) REVERT: D 240 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.6429 (t80) REVERT: D 266 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8414 (tp-100) REVERT: D 306 ASN cc_start: 0.7658 (t0) cc_final: 0.7355 (t0) REVERT: E 14 ASP cc_start: 0.8419 (m-30) cc_final: 0.7745 (p0) REVERT: E 144 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7985 (mp0) REVERT: E 152 ARG cc_start: 0.6246 (ptm-80) cc_final: 0.5740 (mtm110) REVERT: E 203 LYS cc_start: 0.9205 (mmmt) cc_final: 0.8900 (mptt) REVERT: E 266 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8433 (tt0) REVERT: E 297 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7523 (pmm) REVERT: E 306 ASN cc_start: 0.7560 (t0) cc_final: 0.7282 (t0) REVERT: F 14 ASP cc_start: 0.8529 (m-30) cc_final: 0.8010 (t0) REVERT: F 89 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7694 (tt0) REVERT: F 144 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8247 (mp0) REVERT: F 152 ARG cc_start: 0.6172 (ptm-80) cc_final: 0.5941 (ptm-80) REVERT: F 203 LYS cc_start: 0.9226 (mmmt) cc_final: 0.8887 (mptt) REVERT: F 280 TYR cc_start: 0.8163 (t80) cc_final: 0.7635 (m-80) REVERT: F 358 ASN cc_start: 0.9001 (t0) cc_final: 0.8713 (t0) REVERT: G 14 ASP cc_start: 0.8457 (m-30) cc_final: 0.7750 (p0) REVERT: G 128 ARG cc_start: 0.8590 (tmm-80) cc_final: 0.8366 (ttt-90) REVERT: G 144 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7922 (mp0) REVERT: G 152 ARG cc_start: 0.6237 (ptm-80) cc_final: 0.5727 (mtm110) REVERT: G 203 LYS cc_start: 0.9285 (mmmt) cc_final: 0.8916 (mmtt) REVERT: G 266 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8451 (tt0) REVERT: G 317 PHE cc_start: 0.7936 (OUTLIER) cc_final: 0.7625 (m-80) outliers start: 89 outliers final: 53 residues processed: 312 average time/residue: 1.1850 time to fit residues: 420.1411 Evaluate side-chains 312 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 244 time to evaluate : 2.147 ------------------------------------------------------------------------------- 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 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 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 90 GLN Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 124 ASN Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 266 GLN Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 276 ARG Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 124 ASN Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 124 ASN Chi-restraints excluded: chain F residue 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 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 317 PHE 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: 5.9990 chunk 223 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 182 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 222 optimal weight: 30.0000 chunk 48 optimal weight: 0.8980 chunk 155 optimal weight: 9.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 340 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 = 0.3782 r_free = 0.3782 target = 0.124961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.083180 restraints weight = 30639.308| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.45 r_work: 0.2931 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18718 Z= 0.236 Angle : 0.645 11.548 25445 Z= 0.305 Chirality : 0.040 0.214 3045 Planarity : 0.003 0.038 3052 Dihedral : 4.490 59.601 2434 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 4.29 % Allowed : 25.30 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.19), residues: 2198 helix: 2.39 (0.14), residues: 1519 sheet: 0.30 (0.49), residues: 126 loop : -1.19 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 127 HIS 0.003 0.001 HIS G 106 PHE 0.010 0.001 PHE D 12 TYR 0.029 0.001 TYR E 232 ARG 0.007 0.001 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 243 time to evaluate : 2.076 Fit side-chains REVERT: A 14 ASP cc_start: 0.8473 (m-30) cc_final: 0.7618 (p0) REVERT: A 144 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.8012 (mp0) REVERT: A 152 ARG cc_start: 0.6230 (ptm-80) cc_final: 0.5715 (mtm110) REVERT: A 240 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.7195 (m-80) REVERT: A 358 ASN cc_start: 0.8836 (t0) cc_final: 0.8473 (t0) REVERT: B 14 ASP cc_start: 0.8501 (m-30) cc_final: 0.7827 (p0) REVERT: B 144 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8030 (mp0) REVERT: B 152 ARG cc_start: 0.6270 (ptm-80) cc_final: 0.5787 (mtm110) REVERT: B 203 LYS cc_start: 0.9175 (mmmt) cc_final: 0.8809 (mmtt) REVERT: B 240 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.7380 (m-80) REVERT: B 266 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8333 (tt0) REVERT: B 306 ASN cc_start: 0.7512 (t0) cc_final: 0.7263 (t0) REVERT: B 358 ASN cc_start: 0.8890 (t0) cc_final: 0.8530 (t0) REVERT: C 14 ASP cc_start: 0.8443 (m-30) cc_final: 0.7730 (p0) REVERT: C 144 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7985 (mp0) REVERT: C 152 ARG cc_start: 0.6092 (ptm-80) cc_final: 0.5613 (mtm110) REVERT: C 200 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8350 (mm-40) REVERT: C 297 MET cc_start: 0.8220 (pmm) cc_final: 0.7944 (pmt) REVERT: C 306 ASN cc_start: 0.7658 (t0) cc_final: 0.7407 (t0) REVERT: D 14 ASP cc_start: 0.8350 (m-30) cc_final: 0.7610 (p0) REVERT: D 152 ARG cc_start: 0.6199 (ptm-80) cc_final: 0.5687 (mtm110) REVERT: D 200 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8422 (mm-40) REVERT: D 240 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.6351 (t80) REVERT: D 266 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8485 (tp-100) REVERT: D 306 ASN cc_start: 0.7660 (t0) cc_final: 0.7360 (t0) REVERT: D 317 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.7368 (m-80) REVERT: E 14 ASP cc_start: 0.8408 (m-30) cc_final: 0.7719 (p0) REVERT: E 144 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7997 (mp0) REVERT: E 152 ARG cc_start: 0.6199 (ptm-80) cc_final: 0.5709 (mtm110) REVERT: E 203 LYS cc_start: 0.9212 (mmmt) cc_final: 0.8895 (mptt) REVERT: E 266 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8472 (tt0) REVERT: E 297 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7520 (pmm) REVERT: E 306 ASN cc_start: 0.7575 (t0) cc_final: 0.7271 (t0) REVERT: F 14 ASP cc_start: 0.8534 (m-30) cc_final: 0.7998 (t0) REVERT: F 152 ARG cc_start: 0.6161 (ptm-80) cc_final: 0.5928 (ptm-80) REVERT: F 203 LYS cc_start: 0.9231 (mmmt) cc_final: 0.8900 (mptt) REVERT: F 266 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8314 (tt0) REVERT: F 280 TYR cc_start: 0.8169 (t80) cc_final: 0.7605 (m-80) REVERT: F 358 ASN cc_start: 0.9033 (t0) cc_final: 0.8735 (t0) REVERT: G 14 ASP cc_start: 0.8484 (m-30) cc_final: 0.7773 (p0) REVERT: G 128 ARG cc_start: 0.8584 (tmm-80) cc_final: 0.8358 (ttt-90) REVERT: G 144 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7938 (mp0) REVERT: G 152 ARG cc_start: 0.6221 (ptm-80) cc_final: 0.5716 (mtm110) REVERT: G 203 LYS cc_start: 0.9280 (mmmt) cc_final: 0.8912 (mmtt) REVERT: G 266 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8464 (tt0) REVERT: G 317 PHE cc_start: 0.7922 (OUTLIER) cc_final: 0.7604 (m-80) outliers start: 88 outliers final: 52 residues processed: 309 average time/residue: 1.1751 time to fit residues: 412.3182 Evaluate side-chains 307 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 239 time to evaluate : 2.157 ------------------------------------------------------------------------------- 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 101 VAL Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 124 ASN Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 266 GLN 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 266 GLN Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 124 ASN Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 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 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: 4.9990 chunk 183 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 21 optimal weight: 0.0270 chunk 80 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 355 ASN C 266 GLN C 340 ASN C 355 ASN D 355 ASN E 355 ASN F 340 ASN G 56 GLN G 355 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.126829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.085213 restraints weight = 30499.112| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.46 r_work: 0.2973 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18718 Z= 0.172 Angle : 0.641 11.381 25445 Z= 0.303 Chirality : 0.039 0.207 3045 Planarity : 0.003 0.031 3052 Dihedral : 4.412 57.189 2434 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.51 % Allowed : 26.28 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.27 (0.19), residues: 2198 helix: 2.50 (0.14), residues: 1512 sheet: 0.25 (0.49), residues: 126 loop : -1.09 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 74 HIS 0.002 0.001 HIS A 106 PHE 0.010 0.001 PHE D 12 TYR 0.028 0.001 TYR E 232 ARG 0.007 0.001 ARG D 29 ********************** 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 324 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 252 time to evaluate : 2.306 Fit side-chains REVERT: A 14 ASP cc_start: 0.8459 (m-30) cc_final: 0.7527 (p0) REVERT: A 144 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: A 152 ARG cc_start: 0.6234 (ptm-80) cc_final: 0.5712 (mtm110) REVERT: A 240 PHE cc_start: 0.7571 (OUTLIER) cc_final: 0.6949 (m-80) REVERT: A 280 TYR cc_start: 0.8207 (t80) cc_final: 0.7627 (m-80) REVERT: A 358 ASN cc_start: 0.8847 (t0) cc_final: 0.8483 (t0) REVERT: B 14 ASP cc_start: 0.8456 (m-30) cc_final: 0.7817 (p0) REVERT: B 144 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8032 (mp0) REVERT: B 152 ARG cc_start: 0.6271 (ptm-80) cc_final: 0.5751 (mtm110) REVERT: B 203 LYS cc_start: 0.9204 (mmmt) cc_final: 0.8845 (mmtt) REVERT: B 240 PHE cc_start: 0.7622 (OUTLIER) cc_final: 0.7375 (m-80) REVERT: B 306 ASN cc_start: 0.7560 (t0) cc_final: 0.7295 (t0) REVERT: B 358 ASN cc_start: 0.8935 (t0) cc_final: 0.8537 (t0) REVERT: C 14 ASP cc_start: 0.8430 (m-30) cc_final: 0.7635 (p0) REVERT: C 144 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8049 (mp0) REVERT: C 152 ARG cc_start: 0.6098 (ptm-80) cc_final: 0.5610 (mtm110) REVERT: C 200 GLN cc_start: 0.8552 (mm-40) cc_final: 0.8335 (mm-40) REVERT: C 297 MET cc_start: 0.8197 (pmm) cc_final: 0.7914 (pmt) REVERT: C 306 ASN cc_start: 0.7674 (t0) cc_final: 0.7423 (t0) REVERT: C 352 VAL cc_start: 0.8821 (p) cc_final: 0.8607 (t) REVERT: D 14 ASP cc_start: 0.8330 (m-30) cc_final: 0.7631 (p0) REVERT: D 152 ARG cc_start: 0.6309 (ptm-80) cc_final: 0.5768 (mtm110) REVERT: D 200 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8397 (mm-40) REVERT: D 240 PHE cc_start: 0.7711 (OUTLIER) cc_final: 0.6349 (t80) REVERT: D 266 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8407 (tp-100) REVERT: D 306 ASN cc_start: 0.7669 (t0) cc_final: 0.7401 (t0) REVERT: E 14 ASP cc_start: 0.8391 (m-30) cc_final: 0.7735 (p0) REVERT: E 144 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: E 152 ARG cc_start: 0.6152 (ptm-80) cc_final: 0.5721 (mtm110) REVERT: E 203 LYS cc_start: 0.9222 (mmmt) cc_final: 0.8916 (mptt) REVERT: E 266 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8422 (tt0) REVERT: E 306 ASN cc_start: 0.7554 (t0) cc_final: 0.7268 (t0) REVERT: F 14 ASP cc_start: 0.8511 (m-30) cc_final: 0.7981 (t0) REVERT: F 152 ARG cc_start: 0.6109 (ptm-80) cc_final: 0.5858 (ptm-80) REVERT: F 203 LYS cc_start: 0.9248 (mmmt) cc_final: 0.8908 (mptt) REVERT: F 266 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8238 (tt0) REVERT: F 280 TYR cc_start: 0.8140 (t80) cc_final: 0.7600 (m-80) REVERT: F 358 ASN cc_start: 0.9071 (t0) cc_final: 0.8791 (t0) REVERT: G 14 ASP cc_start: 0.8457 (m-30) cc_final: 0.7752 (p0) REVERT: G 128 ARG cc_start: 0.8588 (tmm-80) cc_final: 0.8362 (ttt-90) REVERT: G 144 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: G 152 ARG cc_start: 0.6184 (ptm-80) cc_final: 0.5717 (mtm110) REVERT: G 266 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8458 (tt0) REVERT: G 317 PHE cc_start: 0.7889 (OUTLIER) cc_final: 0.7576 (m-80) outliers start: 72 outliers final: 51 residues processed: 307 average time/residue: 1.1962 time to fit residues: 416.2946 Evaluate side-chains 306 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 242 time to evaluate : 1.987 ------------------------------------------------------------------------------- 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 101 VAL 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 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 D residue 30 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 124 ASN Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 266 GLN Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 276 ARG Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 124 ASN Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 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 202 LEU Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 266 GLN Chi-restraints excluded: chain G residue 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 78 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 93 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 chunk 217 optimal weight: 0.7980 chunk 204 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 340 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 = 0.3784 r_free = 0.3784 target = 0.125107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.082728 restraints weight = 30567.699| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.48 r_work: 0.2931 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18718 Z= 0.238 Angle : 0.675 12.354 25445 Z= 0.319 Chirality : 0.041 0.214 3045 Planarity : 0.003 0.032 3052 Dihedral : 4.317 55.066 2434 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.80 % Allowed : 25.99 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.19), residues: 2198 helix: 2.40 (0.14), residues: 1519 sheet: 0.25 (0.49), residues: 126 loop : -1.15 (0.29), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 127 HIS 0.003 0.001 HIS B 106 PHE 0.012 0.001 PHE E 15 TYR 0.030 0.001 TYR E 232 ARG 0.008 0.001 ARG C 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11612.82 seconds wall clock time: 207 minutes 5.26 seconds (12425.26 seconds total)