Starting phenix.real_space_refine on Sat Sep 12 16:38:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xgc_22180/09_2026/6xgc_22180.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xgc_22180/09_2026/6xgc_22180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xgc_22180/09_2026/6xgc_22180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xgc_22180/09_2026/6xgc_22180.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6xgc_22180/09_2026/6xgc_22180.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xgc_22180/09_2026/6xgc_22180.cif" model { file = "/net/cci-nas-00/data/ceres_data/6xgc_22180/09_2026/6xgc_22180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xgc_22180/09_2026/6xgc_22180.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 10668 2.51 5 N 2916 2.21 5 O 3387 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17040 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2528 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 18, 'TRANS': 304} Chain: "B" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 1, 'TRANS': 162} Chain: "M" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 925 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "N" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 790 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, E, D, F, H, I, L, J, K, O Time building chain proxies: 3.55, per 1000 atoms: 0.21 Number of scatterers: 17040 At special positions: 0 Unit cell: (124.962, 131.316, 150.378, 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 69 16.00 O 3387 8.00 N 2916 7.00 C 10668 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.08 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 285 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 77 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 146 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 313 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 29 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=1.96 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=2.06 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 285 " distance=2.03 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 285 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 77 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS C 100 " - pdb=" SG CYS C 146 " distance=2.03 Simple disulfide: pdb=" SG CYS E 100 " - pdb=" SG CYS E 146 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 313 " distance=2.03 Simple disulfide: pdb=" SG CYS E 289 " - pdb=" SG CYS E 313 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 29 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 29 " - pdb=" SG CYS J 96 " 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 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 403 " - " ASN A 286 " " NAG A 404 " - " ASN A 297 " " NAG A 405 " - " ASN A 33 " " NAG A 406 " - " ASN A 21 " " NAG B 301 " - " ASN B 154 " " NAG C 403 " - " ASN C 286 " " NAG C 404 " - " ASN C 297 " " NAG C 405 " - " ASN C 33 " " NAG C 406 " - " ASN C 21 " " NAG D 301 " - " ASN D 154 " " NAG E 403 " - " ASN E 286 " " NAG E 404 " - " ASN E 297 " " NAG E 405 " - " ASN E 33 " " NAG E 406 " - " ASN E 21 " " NAG F 301 " - " ASN F 154 " " NAG G 1 " - " ASN A 97 " " NAG K 1 " - " ASN C 97 " " NAG O 1 " - " ASN E 97 " Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 676.0 milliseconds 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3924 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 54 sheets defined 19.9% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 66 through 72 Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 194 through 203 Processing helix chain 'B' and resid 37 through 58 Processing helix chain 'B' and resid 74 through 127 Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 158 through 171 removed outlier: 4.003A pdb=" N TYR B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 32 through 37 removed outlier: 3.742A pdb=" N GLY N 37 " --> pdb=" O SER N 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 72 Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 194 through 203 Processing helix chain 'D' and resid 37 through 58 Processing helix chain 'D' and resid 74 through 127 Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 158 through 171 removed outlier: 4.002A pdb=" N TYR D 162 " --> pdb=" O ASP D 158 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU D 164 " --> pdb=" O PRO D 160 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLU D 165 " --> pdb=" O LYS D 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 32 through 37 removed outlier: 3.744A pdb=" N GLY L 37 " --> pdb=" O SER L 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 72 Processing helix chain 'E' and resid 74 through 78 Processing helix chain 'E' and resid 107 through 115 Processing helix chain 'E' and resid 194 through 203 Processing helix chain 'F' and resid 37 through 58 Processing helix chain 'F' and resid 74 through 127 Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 158 through 171 removed outlier: 4.002A pdb=" N TYR F 162 " --> pdb=" O ASP F 158 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLU F 165 " --> pdb=" O LYS F 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'J' and resid 32 through 37 removed outlier: 3.743A pdb=" N GLY J 37 " --> pdb=" O SER J 33 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 36 removed outlier: 4.104A pdb=" N GLY B 23 " --> pdb=" O GLY A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 53 removed outlier: 5.930A pdb=" N LEU A 51 " --> pdb=" O HIS A 283 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N CYS A 285 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 60 through 61 removed outlier: 6.553A pdb=" N LEU A 60 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE A 89 " --> pdb=" O ILE A 276 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 122 through 124 removed outlier: 8.041A pdb=" N LEU A 186 " --> pdb=" O PRO A 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA9, first strand: chain 'A' and resid 143 through 148 removed outlier: 4.649A pdb=" N CYS A 146 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 171 through 176 Processing sheet with id=AB2, first strand: chain 'A' and resid 289 through 290 removed outlier: 3.686A pdb=" N CYS A 289 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 310 through 311 removed outlier: 3.882A pdb=" N THR B 64 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.438A pdb=" N GLY M 10 " --> pdb=" O THR M 124 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 100 through 104 removed outlier: 3.670A pdb=" N GLY M 100 " --> pdb=" O ASN M 111 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 16 through 18 removed outlier: 6.417A pdb=" N TRP N 43 " --> pdb=" O LEU N 55 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 16 through 18 Processing sheet with id=AB9, first strand: chain 'N' and resid 25 through 30 Processing sheet with id=AC1, first strand: chain 'D' and resid 31 through 36 removed outlier: 4.170A pdb=" N GLY D 23 " --> pdb=" O GLY C 16 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AC3, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC4, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC5, first strand: chain 'C' and resid 51 through 53 removed outlier: 5.930A pdb=" N LEU C 51 " --> pdb=" O HIS C 283 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N CYS C 285 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.552A pdb=" N LEU C 60 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE C 89 " --> pdb=" O ILE C 276 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 122 through 124 removed outlier: 8.039A pdb=" N LEU C 186 " --> pdb=" O PRO C 261 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 122 through 124 Processing sheet with id=AC9, first strand: chain 'C' and resid 143 through 148 removed outlier: 4.649A pdb=" N CYS C 146 " --> pdb=" O SER C 153 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 171 through 176 Processing sheet with id=AD2, first strand: chain 'C' and resid 289 through 290 removed outlier: 3.686A pdb=" N CYS C 289 " --> pdb=" O ILE C 296 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 310 through 311 removed outlier: 3.972A pdb=" N THR D 64 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.439A pdb=" N GLY H 10 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 100 through 104 removed outlier: 3.668A pdb=" N GLY H 100 " --> pdb=" O ASN H 111 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 16 through 18 removed outlier: 6.416A pdb=" N TRP L 43 " --> pdb=" O LEU L 55 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 16 through 18 Processing sheet with id=AD9, first strand: chain 'L' and resid 25 through 30 Processing sheet with id=AE1, first strand: chain 'F' and resid 31 through 36 removed outlier: 4.086A pdb=" N GLY F 23 " --> pdb=" O GLY E 16 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 25 through 26 Processing sheet with id=AE3, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AE4, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AE5, first strand: chain 'E' and resid 51 through 53 removed outlier: 5.931A pdb=" N LEU E 51 " --> pdb=" O HIS E 283 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N CYS E 285 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 60 through 61 removed outlier: 6.552A pdb=" N LEU E 60 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE E 89 " --> pdb=" O ILE E 276 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'E' and resid 122 through 124 removed outlier: 8.041A pdb=" N LEU E 186 " --> pdb=" O PRO E 261 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 122 through 124 Processing sheet with id=AE9, first strand: chain 'E' and resid 143 through 148 removed outlier: 4.649A pdb=" N CYS E 146 " --> pdb=" O SER E 153 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 171 through 176 Processing sheet with id=AF2, first strand: chain 'E' and resid 289 through 290 removed outlier: 3.687A pdb=" N CYS E 289 " --> pdb=" O ILE E 296 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 310 through 311 removed outlier: 3.868A pdb=" N THR F 64 " --> pdb=" O GLY E 311 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.438A pdb=" N GLY I 10 " --> pdb=" O THR I 124 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 100 through 104 removed outlier: 3.671A pdb=" N GLY I 100 " --> pdb=" O ASN I 111 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 16 through 18 removed outlier: 6.415A pdb=" N TRP J 43 " --> pdb=" O LEU J 55 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 16 through 18 Processing sheet with id=AF9, first strand: chain 'J' and resid 25 through 30 738 hydrogen bonds defined for protein. 1926 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: 3.13 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5547 1.34 - 1.46: 3563 1.46 - 1.58: 8218 1.58 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 17418 Sorted by residual: bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.23e+00 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.11e+00 bond pdb=" C1 NAG A 403 " pdb=" O5 NAG A 403 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.90e+00 bond pdb=" C1 NAG B 301 " pdb=" O5 NAG B 301 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.90e+00 ... (remaining 17413 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.94: 22761 0.94 - 1.88: 618 1.88 - 2.83: 189 2.83 - 3.77: 36 3.77 - 4.71: 12 Bond angle restraints: 23616 Sorted by residual: angle pdb=" C LEU F 126 " pdb=" N LYS F 127 " pdb=" CA LYS F 127 " ideal model delta sigma weight residual 121.54 126.11 -4.57 1.91e+00 2.74e-01 5.72e+00 angle pdb=" C LEU D 126 " pdb=" N LYS D 127 " pdb=" CA LYS D 127 " ideal model delta sigma weight residual 121.54 126.07 -4.53 1.91e+00 2.74e-01 5.62e+00 angle pdb=" C LEU B 126 " pdb=" N LYS B 127 " pdb=" CA LYS B 127 " ideal model delta sigma weight residual 121.54 126.00 -4.46 1.91e+00 2.74e-01 5.45e+00 angle pdb=" C GLY E 165 " pdb=" N ASN E 166 " pdb=" CA ASN E 166 " ideal model delta sigma weight residual 121.54 125.25 -3.71 1.91e+00 2.74e-01 3.78e+00 angle pdb=" C GLY C 165 " pdb=" N ASN C 166 " pdb=" CA ASN C 166 " ideal model delta sigma weight residual 121.54 125.24 -3.70 1.91e+00 2.74e-01 3.75e+00 ... (remaining 23611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 9873 17.31 - 34.63: 246 34.63 - 51.94: 36 51.94 - 69.25: 3 69.25 - 86.57: 9 Dihedral angle restraints: 10167 sinusoidal: 3996 harmonic: 6171 Sorted by residual: dihedral pdb=" CB GLU C 109 " pdb=" CG GLU C 109 " pdb=" CD GLU C 109 " pdb=" OE1 GLU C 109 " ideal model delta sinusoidal sigma weight residual 0.00 -86.57 86.57 1 3.00e+01 1.11e-03 1.00e+01 dihedral pdb=" CB GLU A 109 " pdb=" CG GLU A 109 " pdb=" CD GLU A 109 " pdb=" OE1 GLU A 109 " ideal model delta sinusoidal sigma weight residual 0.00 -86.56 86.56 1 3.00e+01 1.11e-03 1.00e+01 dihedral pdb=" CB GLU E 109 " pdb=" CG GLU E 109 " pdb=" CD GLU E 109 " pdb=" OE1 GLU E 109 " ideal model delta sinusoidal sigma weight residual 0.00 -86.54 86.54 1 3.00e+01 1.11e-03 1.00e+01 ... (remaining 10164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1561 0.025 - 0.050: 664 0.050 - 0.076: 174 0.076 - 0.101: 108 0.101 - 0.126: 115 Chirality restraints: 2622 Sorted by residual: chirality pdb=" CA ILE A 176 " pdb=" N ILE A 176 " pdb=" C ILE A 176 " pdb=" CB ILE A 176 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" C1 NAG C 406 " pdb=" ND2 ASN C 21 " pdb=" C2 NAG C 406 " pdb=" O5 NAG C 406 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA ILE E 176 " pdb=" N ILE E 176 " pdb=" C ILE E 176 " pdb=" CB ILE E 176 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 ... (remaining 2619 not shown) Planarity restraints: 3045 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 291 " -0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO A 292 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 292 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 292 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 291 " -0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO E 292 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO E 292 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 292 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 291 " 0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO C 292 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 292 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 292 " 0.019 5.00e-02 4.00e+02 ... (remaining 3042 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1694 2.75 - 3.29: 15900 3.29 - 3.83: 28382 3.83 - 4.36: 31425 4.36 - 4.90: 56507 Nonbonded interactions: 133908 Sorted by model distance: nonbonded pdb=" OG SER J 73 " pdb=" OG SER J 80 " model vdw 2.215 3.040 nonbonded pdb=" OG SER N 73 " pdb=" OG SER N 80 " model vdw 2.216 3.040 nonbonded pdb=" OG SER L 73 " pdb=" OG SER L 80 " model vdw 2.217 3.040 nonbonded pdb=" O TYR B 159 " pdb=" OG SER B 163 " model vdw 2.286 3.040 nonbonded pdb=" O TYR D 159 " pdb=" OG SER D 163 " model vdw 2.287 3.040 ... (remaining 133903 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'M' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'N' selection = chain 'L' selection = chain 'J' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.710 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 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 0.073 17463 Z= 0.127 Angle : 0.449 6.740 23727 Z= 0.238 Chirality : 0.040 0.126 2622 Planarity : 0.003 0.034 3027 Dihedral : 7.789 86.567 6171 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.16 % Allowed : 3.64 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.19), residues: 2133 helix: 4.15 (0.25), residues: 351 sheet: 1.15 (0.24), residues: 519 loop : -0.06 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 72 TYR 0.007 0.001 TYR F 94 PHE 0.005 0.001 PHE A 121 TRP 0.005 0.001 TRP E 133 HIS 0.004 0.000 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.12 (17418) covalent geometry : angle 0.43316 / 0.24 (23616) SS BOND : bond 0.01892 / 1.42 ( 24) SS BOND : angle 0.73851 / 0.56 ( 48) hydrogen bonds : bond 0.14255 / 9.36 ( 702) hydrogen bonds : angle 5.75995 / 3.93 ( 1926) link_BETA1-4 : bond 0.00803 / 0.40 ( 3) link_BETA1-4 : angle 5.49846 / 2.94 ( 9) link_NAG-ASN : bond 0.00176 / 0.11 ( 18) link_NAG-ASN : angle 0.96541 / 0.63 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 742 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 LEU cc_start: 0.9253 (mt) cc_final: 0.8983 (mp) REVERT: A 300 LEU cc_start: 0.8719 (mt) cc_final: 0.8299 (mt) REVERT: B 17 MET cc_start: 0.8247 (ttp) cc_final: 0.8016 (ttp) REVERT: B 19 ASP cc_start: 0.8801 (p0) cc_final: 0.8598 (p0) REVERT: B 26 HIS cc_start: 0.7671 (p90) cc_final: 0.7422 (p90) REVERT: B 38 LEU cc_start: 0.8215 (mt) cc_final: 0.7944 (mt) REVERT: B 90 ASP cc_start: 0.6534 (m-30) cc_final: 0.6088 (m-30) REVERT: B 99 LEU cc_start: 0.8449 (tp) cc_final: 0.8240 (tp) REVERT: M 36 TRP cc_start: 0.8377 (m100) cc_final: 0.7698 (m100) REVERT: M 47 TRP cc_start: 0.8490 (t60) cc_final: 0.8282 (t60) REVERT: M 48 ILE cc_start: 0.8494 (mm) cc_final: 0.6775 (mm) REVERT: N 105 ASN cc_start: 0.7581 (m-40) cc_final: 0.7191 (m110) REVERT: C 204 ASN cc_start: 0.8741 (m-40) cc_final: 0.8497 (m-40) REVERT: C 230 VAL cc_start: 0.8622 (t) cc_final: 0.8414 (p) REVERT: C 236 ARG cc_start: 0.8135 (mmt-90) cc_final: 0.7934 (mmt-90) REVERT: C 262 ARG cc_start: 0.8385 (ttt180) cc_final: 0.8144 (ttt-90) REVERT: C 263 TYR cc_start: 0.7903 (m-80) cc_final: 0.7634 (m-80) REVERT: D 26 HIS cc_start: 0.7970 (p90) cc_final: 0.7307 (p90) REVERT: D 138 PHE cc_start: 0.8338 (m-80) cc_final: 0.8079 (m-80) REVERT: D 147 THR cc_start: 0.8975 (m) cc_final: 0.8747 (p) REVERT: H 36 TRP cc_start: 0.8464 (m100) cc_final: 0.8224 (m100) REVERT: H 48 ILE cc_start: 0.8495 (mm) cc_final: 0.8276 (mm) REVERT: H 94 TYR cc_start: 0.7169 (m-80) cc_final: 0.6961 (m-10) REVERT: L 93 ASP cc_start: 0.8351 (m-30) cc_final: 0.8081 (m-30) REVERT: L 113 ARG cc_start: 0.6793 (tpp80) cc_final: 0.6522 (tpp-160) REVERT: E 204 ASN cc_start: 0.8576 (m-40) cc_final: 0.8363 (m110) REVERT: E 300 LEU cc_start: 0.8675 (mt) cc_final: 0.8473 (mt) REVERT: F 26 HIS cc_start: 0.8135 (p90) cc_final: 0.7561 (p90) REVERT: F 27 GLN cc_start: 0.8415 (tt0) cc_final: 0.8211 (tm-30) REVERT: F 99 LEU cc_start: 0.8121 (tp) cc_final: 0.7505 (tt) REVERT: F 114 ASN cc_start: 0.8663 (m-40) cc_final: 0.8397 (m110) REVERT: I 34 MET cc_start: 0.7986 (mmm) cc_final: 0.7436 (mmt) REVERT: I 47 TRP cc_start: 0.8378 (t60) cc_final: 0.8112 (t60) outliers start: 3 outliers final: 3 residues processed: 745 average time/residue: 0.1390 time to fit residues: 153.9526 Evaluate side-chains 405 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 402 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 HIS A 238 ASN A 290 GLN ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN M 39 GLN N 40 HIS N 45 GLN N 58 ASN N 87 GLN C 238 ASN C 257 ASN C 290 GLN D 114 ASN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 HIS L 45 GLN L 58 ASN ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 238 ASN E 290 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN J 40 HIS J 45 GLN J 46 GLN J 58 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.113725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.095718 restraints weight = 35436.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.097063 restraints weight = 24033.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.098402 restraints weight = 18468.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.099435 restraints weight = 12929.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.099689 restraints weight = 11391.521| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 17463 Z= 0.134 Angle : 0.576 6.991 23727 Z= 0.298 Chirality : 0.043 0.200 2622 Planarity : 0.004 0.036 3027 Dihedral : 3.334 15.585 2319 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.16 % Allowed : 1.79 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.18), residues: 2133 helix: 3.28 (0.25), residues: 360 sheet: 1.30 (0.24), residues: 465 loop : -0.17 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 112 TYR 0.019 0.001 TYR M 94 PHE 0.019 0.002 PHE A 210 TRP 0.021 0.002 TRP N 43 HIS 0.010 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (17418) covalent geometry : angle 0.56488 / 0.29 (23616) SS BOND : bond 0.00522 / 0.41 ( 24) SS BOND : angle 1.57411 / 1.08 ( 48) hydrogen bonds : bond 0.04171 / 2.73 ( 702) hydrogen bonds : angle 4.97207 / 3.38 ( 1926) link_BETA1-4 : bond 0.00603 / 0.30 ( 3) link_BETA1-4 : angle 4.34185 / 2.26 ( 9) link_NAG-ASN : bond 0.00193 / 0.11 ( 18) link_NAG-ASN : angle 1.04146 / 0.67 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 505 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 ASP cc_start: 0.8944 (p0) cc_final: 0.8740 (p0) REVERT: B 99 LEU cc_start: 0.8518 (tp) cc_final: 0.8239 (tp) REVERT: B 103 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7518 (tp30) REVERT: B 147 THR cc_start: 0.8844 (p) cc_final: 0.8453 (p) REVERT: M 36 TRP cc_start: 0.8434 (m100) cc_final: 0.7257 (m100) REVERT: M 46 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7365 (tm-30) REVERT: M 47 TRP cc_start: 0.8534 (t60) cc_final: 0.8302 (t60) REVERT: M 82 GLN cc_start: 0.7185 (tp40) cc_final: 0.6939 (tm-30) REVERT: M 87 ARG cc_start: 0.7323 (ptp-110) cc_final: 0.7024 (mtm-85) REVERT: M 90 ASP cc_start: 0.8118 (m-30) cc_final: 0.7811 (m-30) REVERT: M 99 ASP cc_start: 0.7721 (m-30) cc_final: 0.7359 (m-30) REVERT: N 46 GLN cc_start: 0.8432 (tt0) cc_final: 0.8038 (tt0) REVERT: N 93 ASP cc_start: 0.8383 (m-30) cc_final: 0.7469 (p0) REVERT: N 105 ASN cc_start: 0.7747 (m-40) cc_final: 0.7404 (m-40) REVERT: C 155 TYR cc_start: 0.8066 (m-80) cc_final: 0.7808 (m-80) REVERT: C 204 ASN cc_start: 0.8950 (m-40) cc_final: 0.8575 (m-40) REVERT: D 17 MET cc_start: 0.8193 (ttp) cc_final: 0.7989 (ttp) REVERT: D 30 GLN cc_start: 0.8539 (mp10) cc_final: 0.8302 (mp10) REVERT: D 105 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7279 (mm-30) REVERT: D 114 ASN cc_start: 0.8789 (m-40) cc_final: 0.8383 (m-40) REVERT: D 147 THR cc_start: 0.9280 (m) cc_final: 0.8627 (p) REVERT: H 36 TRP cc_start: 0.8424 (m100) cc_final: 0.7795 (m100) REVERT: H 76 LYS cc_start: 0.8500 (mtmt) cc_final: 0.8192 (ptpt) REVERT: H 83 MET cc_start: 0.7629 (mtt) cc_final: 0.7034 (mtt) REVERT: H 87 ARG cc_start: 0.7893 (mtp85) cc_final: 0.7606 (mtm-85) REVERT: H 94 TYR cc_start: 0.7479 (m-80) cc_final: 0.6995 (m-10) REVERT: H 99 ASP cc_start: 0.7867 (m-30) cc_final: 0.7483 (m-30) REVERT: L 27 ILE cc_start: 0.8949 (mt) cc_final: 0.8686 (mt) REVERT: L 43 TRP cc_start: 0.7778 (m100) cc_final: 0.7565 (m-10) REVERT: L 81 LEU cc_start: 0.8953 (tt) cc_final: 0.7921 (tt) REVERT: F 17 MET cc_start: 0.8452 (tmm) cc_final: 0.8211 (tmm) REVERT: F 26 HIS cc_start: 0.8355 (p90) cc_final: 0.7427 (p90) REVERT: F 105 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7368 (mm-30) REVERT: F 114 ASN cc_start: 0.8813 (m-40) cc_final: 0.8461 (m110) REVERT: I 6 GLU cc_start: 0.8480 (mp0) cc_final: 0.8230 (mp0) REVERT: I 34 MET cc_start: 0.8042 (mmm) cc_final: 0.7454 (mmt) REVERT: I 47 TRP cc_start: 0.8463 (t60) cc_final: 0.7893 (t60) REVERT: I 48 ILE cc_start: 0.8747 (mm) cc_final: 0.7903 (mt) REVERT: I 68 PHE cc_start: 0.7984 (m-10) cc_final: 0.7587 (m-10) REVERT: I 82 GLN cc_start: 0.7268 (tp40) cc_final: 0.6904 (tm-30) outliers start: 3 outliers final: 0 residues processed: 506 average time/residue: 0.1313 time to fit residues: 103.0828 Evaluate side-chains 364 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 136 optimal weight: 10.0000 chunk 163 optimal weight: 0.0000 chunk 102 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 GLN B 124 ASN B 125 GLN B 142 HIS ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 HIS L 45 GLN ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 238 ASN E 257 ASN E 290 GLN F 25 HIS F 62 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 HIS ** J 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.103228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.085275 restraints weight = 36489.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.085789 restraints weight = 25548.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.087018 restraints weight = 20299.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.088473 restraints weight = 15106.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.088695 restraints weight = 13285.541| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 17463 Z= 0.283 Angle : 0.692 10.182 23727 Z= 0.364 Chirality : 0.045 0.276 2622 Planarity : 0.005 0.051 3027 Dihedral : 4.188 28.135 2319 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.33 % Allowed : 4.02 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.18), residues: 2133 helix: 2.15 (0.26), residues: 357 sheet: 1.10 (0.23), residues: 489 loop : -0.50 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 112 TYR 0.028 0.002 TYR H 112 PHE 0.035 0.003 PHE A 210 TRP 0.016 0.002 TRP H 47 HIS 0.007 0.002 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.28 (17418) covalent geometry : angle 0.68096 / 0.36 (23616) SS BOND : bond 0.00568 / 0.40 ( 24) SS BOND : angle 1.78358 / 1.08 ( 48) hydrogen bonds : bond 0.04865 / 3.22 ( 702) hydrogen bonds : angle 5.37714 / 3.67 ( 1926) link_BETA1-4 : bond 0.00668 / 0.34 ( 3) link_BETA1-4 : angle 4.18269 / 2.15 ( 9) link_NAG-ASN : bond 0.00236 / 0.14 ( 18) link_NAG-ASN : angle 1.29834 / 0.87 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 442 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 TYR cc_start: 0.7947 (t80) cc_final: 0.7742 (t80) REVERT: A 203 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8332 (tm-30) REVERT: B 27 GLN cc_start: 0.8366 (tp40) cc_final: 0.8007 (tp-100) REVERT: B 32 SER cc_start: 0.8962 (p) cc_final: 0.8707 (p) REVERT: M 36 TRP cc_start: 0.8344 (m100) cc_final: 0.7991 (m100) REVERT: M 46 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7977 (tm-30) REVERT: M 47 TRP cc_start: 0.8647 (t60) cc_final: 0.8264 (t60) REVERT: M 48 ILE cc_start: 0.8629 (mm) cc_final: 0.8275 (mp) REVERT: M 82 GLN cc_start: 0.7389 (tp40) cc_final: 0.7001 (tm-30) REVERT: M 90 ASP cc_start: 0.8256 (m-30) cc_final: 0.7833 (m-30) REVERT: M 99 ASP cc_start: 0.7985 (m-30) cc_final: 0.7758 (m-30) REVERT: N 36 PHE cc_start: 0.7339 (t80) cc_final: 0.6955 (t80) REVERT: C 155 TYR cc_start: 0.8319 (m-80) cc_final: 0.8018 (m-80) REVERT: C 204 ASN cc_start: 0.9084 (m-40) cc_final: 0.8787 (m-40) REVERT: C 241 TRP cc_start: 0.9106 (p-90) cc_final: 0.8866 (p-90) REVERT: D 17 MET cc_start: 0.8571 (ttp) cc_final: 0.8268 (ttp) REVERT: D 30 GLN cc_start: 0.8678 (mp10) cc_final: 0.8475 (mp10) REVERT: D 147 THR cc_start: 0.9259 (m) cc_final: 0.8741 (p) REVERT: H 36 TRP cc_start: 0.8492 (m100) cc_final: 0.7715 (m100) REVERT: H 82 GLN cc_start: 0.7161 (tm-30) cc_final: 0.6848 (tm-30) REVERT: H 90 ASP cc_start: 0.8355 (m-30) cc_final: 0.7947 (m-30) REVERT: L 43 TRP cc_start: 0.8075 (m100) cc_final: 0.7352 (m100) REVERT: E 77 CYS cc_start: 0.5982 (m) cc_final: 0.5772 (m) REVERT: E 155 TYR cc_start: 0.8400 (m-80) cc_final: 0.8116 (m-80) REVERT: E 203 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8399 (tm-30) REVERT: F 17 MET cc_start: 0.8672 (tmm) cc_final: 0.8226 (tmm) REVERT: F 26 HIS cc_start: 0.8523 (p90) cc_final: 0.8243 (p90) REVERT: F 114 ASN cc_start: 0.9058 (m-40) cc_final: 0.8663 (m110) REVERT: I 6 GLU cc_start: 0.8661 (mp0) cc_final: 0.8385 (mp0) REVERT: I 34 MET cc_start: 0.8263 (mmm) cc_final: 0.7825 (mmt) REVERT: I 36 TRP cc_start: 0.8548 (m100) cc_final: 0.8316 (m100) REVERT: I 46 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7485 (tm-30) REVERT: I 48 ILE cc_start: 0.8692 (mm) cc_final: 0.8304 (mm) REVERT: J 43 TRP cc_start: 0.8231 (m100) cc_final: 0.7762 (m100) outliers start: 6 outliers final: 2 residues processed: 444 average time/residue: 0.1165 time to fit residues: 82.8111 Evaluate side-chains 335 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 333 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 192 optimal weight: 5.9990 chunk 200 optimal weight: 9.9990 chunk 125 optimal weight: 0.9990 chunk 190 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 ASN A 290 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 ASN C 290 GLN D 125 GLN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN E 290 GLN F 125 GLN ** J 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.103680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.085434 restraints weight = 36555.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.086023 restraints weight = 26274.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.087211 restraints weight = 20895.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.088820 restraints weight = 15742.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.088994 restraints weight = 13618.862| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 17463 Z= 0.239 Angle : 0.684 12.961 23727 Z= 0.356 Chirality : 0.045 0.283 2622 Planarity : 0.004 0.053 3027 Dihedral : 4.378 35.372 2319 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.05 % Allowed : 2.33 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.17), residues: 2133 helix: 1.81 (0.26), residues: 357 sheet: 0.91 (0.22), residues: 516 loop : -0.76 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 87 TYR 0.038 0.002 TYR I 112 PHE 0.017 0.002 PHE E 220 TRP 0.017 0.002 TRP H 47 HIS 0.010 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.24 (17418) covalent geometry : angle 0.66677 / 0.35 (23616) SS BOND : bond 0.00891 / 0.60 ( 24) SS BOND : angle 2.31611 / 1.29 ( 48) hydrogen bonds : bond 0.04543 / 3.02 ( 702) hydrogen bonds : angle 5.58536 / 3.74 ( 1926) link_BETA1-4 : bond 0.00449 / 0.23 ( 3) link_BETA1-4 : angle 5.19734 / 2.54 ( 9) link_NAG-ASN : bond 0.00201 / 0.14 ( 18) link_NAG-ASN : angle 1.30960 / 0.88 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 414 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 TYR cc_start: 0.8012 (t80) cc_final: 0.7724 (t80) REVERT: B 27 GLN cc_start: 0.8400 (tp40) cc_final: 0.8026 (tp-100) REVERT: B 28 ASN cc_start: 0.9056 (p0) cc_final: 0.8720 (p0) REVERT: M 36 TRP cc_start: 0.8293 (m100) cc_final: 0.7967 (m100) REVERT: M 46 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7836 (tm-30) REVERT: M 47 TRP cc_start: 0.8646 (t60) cc_final: 0.8275 (t60) REVERT: M 48 ILE cc_start: 0.8810 (mm) cc_final: 0.8390 (mt) REVERT: M 82 GLN cc_start: 0.7561 (tp40) cc_final: 0.7036 (tm-30) REVERT: M 87 ARG cc_start: 0.8092 (mtp85) cc_final: 0.7668 (mtm-85) REVERT: M 90 ASP cc_start: 0.8335 (m-30) cc_final: 0.7895 (m-30) REVERT: M 99 ASP cc_start: 0.8296 (m-30) cc_final: 0.7557 (m-30) REVERT: C 108 TYR cc_start: 0.7925 (t80) cc_final: 0.7666 (t80) REVERT: C 204 ASN cc_start: 0.9013 (m-40) cc_final: 0.8717 (m-40) REVERT: D 133 ILE cc_start: 0.8945 (mp) cc_final: 0.8432 (mm) REVERT: D 147 THR cc_start: 0.9297 (m) cc_final: 0.8658 (t) REVERT: H 36 TRP cc_start: 0.8502 (m100) cc_final: 0.7694 (m100) REVERT: H 90 ASP cc_start: 0.8458 (m-30) cc_final: 0.7945 (m-30) REVERT: L 43 TRP cc_start: 0.7872 (m100) cc_final: 0.6214 (m100) REVERT: L 55 LEU cc_start: 0.8983 (mt) cc_final: 0.8632 (mp) REVERT: E 77 CYS cc_start: 0.5774 (m) cc_final: 0.5556 (m) REVERT: E 108 TYR cc_start: 0.8009 (t80) cc_final: 0.7747 (t80) REVERT: E 155 TYR cc_start: 0.8397 (m-80) cc_final: 0.8047 (m-80) REVERT: E 267 MET cc_start: 0.7566 (ttp) cc_final: 0.7332 (ttp) REVERT: F 17 MET cc_start: 0.8759 (tmm) cc_final: 0.8542 (tmm) REVERT: F 114 ASN cc_start: 0.9116 (m-40) cc_final: 0.8884 (m-40) REVERT: F 133 ILE cc_start: 0.9005 (mt) cc_final: 0.8550 (mm) REVERT: I 6 GLU cc_start: 0.8761 (mp0) cc_final: 0.8520 (mp0) REVERT: I 34 MET cc_start: 0.8135 (mmm) cc_final: 0.7713 (mmt) REVERT: I 36 TRP cc_start: 0.8714 (m100) cc_final: 0.8449 (m100) REVERT: I 46 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7453 (tm-30) REVERT: I 48 ILE cc_start: 0.8975 (mm) cc_final: 0.8414 (mm) REVERT: I 82 GLN cc_start: 0.7654 (tp40) cc_final: 0.6910 (tm-30) REVERT: I 87 ARG cc_start: 0.7843 (mtm-85) cc_final: 0.7563 (mtm-85) REVERT: I 90 ASP cc_start: 0.8361 (m-30) cc_final: 0.8054 (m-30) REVERT: J 43 TRP cc_start: 0.8363 (m100) cc_final: 0.7635 (m100) REVERT: J 93 ASP cc_start: 0.7949 (m-30) cc_final: 0.7017 (p0) REVERT: J 94 TYR cc_start: 0.7712 (m-80) cc_final: 0.7373 (m-10) outliers start: 1 outliers final: 0 residues processed: 414 average time/residue: 0.1166 time to fit residues: 77.4904 Evaluate side-chains 319 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 200 optimal weight: 20.0000 chunk 76 optimal weight: 1.9990 chunk 178 optimal weight: 0.7980 chunk 197 optimal weight: 7.9990 chunk 9 optimal weight: 0.6980 chunk 149 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 183 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 HIS ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 GLN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 GLN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 HIS E 290 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.107044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.089097 restraints weight = 35549.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.090321 restraints weight = 23136.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.091482 restraints weight = 18262.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.092097 restraints weight = 12817.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.092134 restraints weight = 12132.164| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 17463 Z= 0.129 Angle : 0.616 9.875 23727 Z= 0.316 Chirality : 0.044 0.174 2622 Planarity : 0.004 0.058 3027 Dihedral : 4.165 33.853 2319 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.05 % Allowed : 1.85 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.17), residues: 2133 helix: 1.91 (0.26), residues: 357 sheet: 1.03 (0.24), residues: 471 loop : -0.67 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 123 TYR 0.026 0.001 TYR I 112 PHE 0.019 0.002 PHE A 210 TRP 0.023 0.001 TRP C 241 HIS 0.009 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (17418) covalent geometry : angle 0.59668 / 0.31 (23616) SS BOND : bond 0.00865 / 0.57 ( 24) SS BOND : angle 2.48011 / 1.36 ( 48) hydrogen bonds : bond 0.04012 / 2.64 ( 702) hydrogen bonds : angle 5.39596 / 3.64 ( 1926) link_BETA1-4 : bond 0.00445 / 0.23 ( 3) link_BETA1-4 : angle 4.94774 / 2.42 ( 9) link_NAG-ASN : bond 0.00149 / 0.08 ( 18) link_NAG-ASN : angle 1.15032 / 0.80 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 405 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 TYR cc_start: 0.7842 (t80) cc_final: 0.7574 (t80) REVERT: A 124 PHE cc_start: 0.8232 (t80) cc_final: 0.8009 (t80) REVERT: B 28 ASN cc_start: 0.8969 (p0) cc_final: 0.8636 (p0) REVERT: B 32 SER cc_start: 0.8806 (p) cc_final: 0.8480 (p) REVERT: B 133 ILE cc_start: 0.8832 (mp) cc_final: 0.8586 (mm) REVERT: M 36 TRP cc_start: 0.8058 (m100) cc_final: 0.7652 (m100) REVERT: M 46 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7848 (tm-30) REVERT: M 47 TRP cc_start: 0.8538 (t60) cc_final: 0.8284 (t60) REVERT: M 48 ILE cc_start: 0.8787 (mm) cc_final: 0.8205 (mt) REVERT: M 82 GLN cc_start: 0.7488 (tp40) cc_final: 0.7007 (tm-30) REVERT: M 87 ARG cc_start: 0.8047 (mtp85) cc_final: 0.7742 (mtm-85) REVERT: M 90 ASP cc_start: 0.8295 (m-30) cc_final: 0.7859 (m-30) REVERT: M 99 ASP cc_start: 0.8408 (m-30) cc_final: 0.7876 (m-30) REVERT: N 99 TRP cc_start: 0.8020 (t-100) cc_final: 0.7124 (t-100) REVERT: N 105 ASN cc_start: 0.7602 (m-40) cc_final: 0.6964 (m-40) REVERT: C 108 TYR cc_start: 0.7848 (t80) cc_final: 0.7431 (t80) REVERT: C 204 ASN cc_start: 0.8987 (m-40) cc_final: 0.8589 (m-40) REVERT: H 32 TYR cc_start: 0.8788 (m-10) cc_final: 0.8527 (m-10) REVERT: H 36 TRP cc_start: 0.8326 (m100) cc_final: 0.7848 (m100) REVERT: H 68 PHE cc_start: 0.8399 (m-10) cc_final: 0.7793 (m-10) REVERT: H 82 GLN cc_start: 0.7326 (tm-30) cc_final: 0.7018 (tm-30) REVERT: H 87 ARG cc_start: 0.7739 (mtm-85) cc_final: 0.7321 (mtm-85) REVERT: H 90 ASP cc_start: 0.8385 (m-30) cc_final: 0.7968 (m-30) REVERT: L 43 TRP cc_start: 0.7743 (m100) cc_final: 0.6370 (m100) REVERT: L 55 LEU cc_start: 0.8919 (mt) cc_final: 0.8598 (mp) REVERT: E 77 CYS cc_start: 0.5804 (m) cc_final: 0.5585 (m) REVERT: E 108 TYR cc_start: 0.7835 (t80) cc_final: 0.7617 (t80) REVERT: E 203 GLN cc_start: 0.8647 (tm-30) cc_final: 0.8247 (tm-30) REVERT: E 267 MET cc_start: 0.7418 (ttp) cc_final: 0.7178 (ttp) REVERT: F 26 HIS cc_start: 0.8457 (p90) cc_final: 0.8203 (p90) REVERT: I 6 GLU cc_start: 0.8786 (mp0) cc_final: 0.8510 (mp0) REVERT: I 46 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7466 (tm-30) REVERT: I 48 ILE cc_start: 0.9003 (mm) cc_final: 0.8480 (mm) REVERT: I 82 GLN cc_start: 0.7578 (tp40) cc_final: 0.6774 (tm-30) REVERT: I 90 ASP cc_start: 0.8328 (m-30) cc_final: 0.8053 (m-30) REVERT: J 43 TRP cc_start: 0.8025 (m100) cc_final: 0.7498 (m100) REVERT: J 94 TYR cc_start: 0.7624 (m-80) cc_final: 0.7395 (m-10) outliers start: 1 outliers final: 0 residues processed: 405 average time/residue: 0.1144 time to fit residues: 74.4449 Evaluate side-chains 326 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 181 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 193 optimal weight: 0.0970 chunk 134 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 ASN A 290 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 ASN C 290 GLN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN L 13 GLN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN E 290 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.108779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.090841 restraints weight = 35689.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.091574 restraints weight = 24044.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.092887 restraints weight = 19608.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.093646 restraints weight = 13867.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.093811 restraints weight = 13129.851| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17463 Z= 0.127 Angle : 0.591 8.526 23727 Z= 0.306 Chirality : 0.043 0.161 2622 Planarity : 0.004 0.053 3027 Dihedral : 4.114 31.272 2319 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.17), residues: 2133 helix: 1.97 (0.26), residues: 357 sheet: 0.94 (0.22), residues: 516 loop : -0.68 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 123 TYR 0.024 0.001 TYR H 94 PHE 0.033 0.001 PHE A 210 TRP 0.023 0.002 TRP E 133 HIS 0.010 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (17418) covalent geometry : angle 0.57451 / 0.30 (23616) SS BOND : bond 0.00470 / 0.30 ( 24) SS BOND : angle 2.20738 / 1.04 ( 48) hydrogen bonds : bond 0.03900 / 2.58 ( 702) hydrogen bonds : angle 5.31244 / 3.57 ( 1926) link_BETA1-4 : bond 0.00359 / 0.18 ( 3) link_BETA1-4 : angle 4.54768 / 2.23 ( 9) link_NAG-ASN : bond 0.00142 / 0.09 ( 18) link_NAG-ASN : angle 1.06538 / 0.74 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 399 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 TYR cc_start: 0.7807 (t80) cc_final: 0.7537 (t80) REVERT: A 124 PHE cc_start: 0.8211 (t80) cc_final: 0.7978 (t80) REVERT: A 237 MET cc_start: 0.8682 (tpp) cc_final: 0.8454 (mpp) REVERT: B 17 MET cc_start: 0.8749 (ttp) cc_final: 0.8057 (ppp) REVERT: B 28 ASN cc_start: 0.8918 (p0) cc_final: 0.8614 (p0) REVERT: M 36 TRP cc_start: 0.7964 (m100) cc_final: 0.7476 (m100) REVERT: M 47 TRP cc_start: 0.8576 (t60) cc_final: 0.8132 (t60) REVERT: M 82 GLN cc_start: 0.7557 (tp40) cc_final: 0.7008 (tm-30) REVERT: M 90 ASP cc_start: 0.8215 (m-30) cc_final: 0.7897 (m-30) REVERT: M 99 ASP cc_start: 0.8056 (m-30) cc_final: 0.7535 (m-30) REVERT: N 13 GLN cc_start: 0.8172 (mt0) cc_final: 0.7937 (pt0) REVERT: N 99 TRP cc_start: 0.8090 (t-100) cc_final: 0.7131 (t-100) REVERT: N 105 ASN cc_start: 0.7613 (m-40) cc_final: 0.6969 (m-40) REVERT: C 44 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7637 (mt-10) REVERT: C 108 TYR cc_start: 0.7856 (t80) cc_final: 0.7591 (t80) REVERT: C 204 ASN cc_start: 0.8915 (m-40) cc_final: 0.8535 (m-40) REVERT: D 37 ASP cc_start: 0.8022 (t70) cc_final: 0.7577 (t70) REVERT: H 36 TRP cc_start: 0.8083 (m100) cc_final: 0.7698 (m100) REVERT: H 90 ASP cc_start: 0.8340 (m-30) cc_final: 0.8016 (m-30) REVERT: L 43 TRP cc_start: 0.7603 (m100) cc_final: 0.6464 (m100) REVERT: L 55 LEU cc_start: 0.8861 (mt) cc_final: 0.8549 (mp) REVERT: E 77 CYS cc_start: 0.5740 (m) cc_final: 0.5493 (m) REVERT: E 108 TYR cc_start: 0.7943 (t80) cc_final: 0.7682 (t80) REVERT: E 124 PHE cc_start: 0.8000 (t80) cc_final: 0.7797 (t80) REVERT: E 155 TYR cc_start: 0.8396 (m-80) cc_final: 0.7978 (m-80) REVERT: E 203 GLN cc_start: 0.8556 (tm-30) cc_final: 0.8179 (tm-30) REVERT: E 267 MET cc_start: 0.7318 (ttp) cc_final: 0.7098 (ttp) REVERT: F 26 HIS cc_start: 0.8436 (p90) cc_final: 0.8188 (p90) REVERT: F 133 ILE cc_start: 0.9042 (mp) cc_final: 0.8638 (mm) REVERT: I 6 GLU cc_start: 0.8758 (mp0) cc_final: 0.8540 (mp0) REVERT: I 32 TYR cc_start: 0.8593 (m-10) cc_final: 0.8294 (m-10) REVERT: I 46 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7795 (tm-30) REVERT: I 48 ILE cc_start: 0.8847 (mm) cc_final: 0.8240 (mm) REVERT: I 82 GLN cc_start: 0.7585 (tp40) cc_final: 0.6790 (tm-30) REVERT: I 90 ASP cc_start: 0.8323 (m-30) cc_final: 0.8018 (m-30) REVERT: J 43 TRP cc_start: 0.7768 (m100) cc_final: 0.7545 (m100) outliers start: 0 outliers final: 0 residues processed: 399 average time/residue: 0.1156 time to fit residues: 74.0189 Evaluate side-chains 316 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 159 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 198 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 HIS A 290 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 GLN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 GLN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.108494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.090709 restraints weight = 35725.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.091537 restraints weight = 24678.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.092735 restraints weight = 20219.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.093549 restraints weight = 14212.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.093592 restraints weight = 13495.088| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17463 Z= 0.132 Angle : 0.595 7.139 23727 Z= 0.310 Chirality : 0.043 0.168 2622 Planarity : 0.004 0.064 3027 Dihedral : 4.147 29.662 2319 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.17), residues: 2133 helix: 1.76 (0.26), residues: 357 sheet: 1.02 (0.23), residues: 501 loop : -0.71 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 87 TYR 0.021 0.001 TYR I 112 PHE 0.026 0.001 PHE A 210 TRP 0.031 0.001 TRP N 43 HIS 0.010 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (17418) covalent geometry : angle 0.58211 / 0.31 (23616) SS BOND : bond 0.00443 / 0.29 ( 24) SS BOND : angle 1.90800 / 0.98 ( 48) hydrogen bonds : bond 0.03956 / 2.62 ( 702) hydrogen bonds : angle 5.25524 / 3.52 ( 1926) link_BETA1-4 : bond 0.00487 / 0.25 ( 3) link_BETA1-4 : angle 4.28036 / 2.11 ( 9) link_NAG-ASN : bond 0.00144 / 0.09 ( 18) link_NAG-ASN : angle 1.09716 / 0.78 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 TYR cc_start: 0.7788 (t80) cc_final: 0.7519 (t80) REVERT: A 237 MET cc_start: 0.8530 (tpp) cc_final: 0.8149 (mpp) REVERT: B 27 GLN cc_start: 0.8333 (tp-100) cc_final: 0.8113 (tp-100) REVERT: B 28 ASN cc_start: 0.8890 (p0) cc_final: 0.8446 (p0) REVERT: B 135 ASN cc_start: 0.7143 (p0) cc_final: 0.6940 (p0) REVERT: M 36 TRP cc_start: 0.7951 (m100) cc_final: 0.7563 (m100) REVERT: M 47 TRP cc_start: 0.8362 (t60) cc_final: 0.8087 (t60) REVERT: M 48 ILE cc_start: 0.8872 (mm) cc_final: 0.8303 (mm) REVERT: M 82 GLN cc_start: 0.7598 (tp40) cc_final: 0.7020 (tm-30) REVERT: M 87 ARG cc_start: 0.7537 (mtm-85) cc_final: 0.7110 (mtm-85) REVERT: M 90 ASP cc_start: 0.8137 (m-30) cc_final: 0.7777 (m-30) REVERT: M 99 ASP cc_start: 0.8339 (m-30) cc_final: 0.7849 (m-30) REVERT: N 46 GLN cc_start: 0.8689 (tp40) cc_final: 0.8439 (tp40) REVERT: N 99 TRP cc_start: 0.8171 (t-100) cc_final: 0.7236 (t-100) REVERT: N 105 ASN cc_start: 0.7660 (m-40) cc_final: 0.7332 (m-40) REVERT: C 44 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7625 (mt-10) REVERT: C 108 TYR cc_start: 0.7936 (t80) cc_final: 0.7620 (t80) REVERT: C 204 ASN cc_start: 0.8908 (m-40) cc_final: 0.8520 (m-40) REVERT: D 37 ASP cc_start: 0.7824 (t70) cc_final: 0.7621 (t0) REVERT: H 48 ILE cc_start: 0.8419 (mm) cc_final: 0.8186 (mm) REVERT: H 82 GLN cc_start: 0.7142 (tm-30) cc_final: 0.6931 (tm-30) REVERT: H 83 MET cc_start: 0.7390 (mtt) cc_final: 0.7174 (mtt) REVERT: H 87 ARG cc_start: 0.7658 (mtm-85) cc_final: 0.7245 (mtm-85) REVERT: H 90 ASP cc_start: 0.8120 (m-30) cc_final: 0.7908 (m-30) REVERT: H 94 TYR cc_start: 0.7373 (m-80) cc_final: 0.7134 (m-10) REVERT: E 77 CYS cc_start: 0.5783 (m) cc_final: 0.5492 (m) REVERT: E 108 TYR cc_start: 0.7962 (t80) cc_final: 0.7740 (t80) REVERT: E 203 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8130 (tm-30) REVERT: F 17 MET cc_start: 0.8705 (tmm) cc_final: 0.8368 (tmm) REVERT: F 26 HIS cc_start: 0.8424 (p90) cc_final: 0.8164 (p90) REVERT: F 27 GLN cc_start: 0.8259 (tp-100) cc_final: 0.8002 (tp40) REVERT: F 133 ILE cc_start: 0.8975 (mp) cc_final: 0.8543 (mm) REVERT: I 6 GLU cc_start: 0.8739 (mp0) cc_final: 0.8537 (mp0) REVERT: I 32 TYR cc_start: 0.8404 (m-10) cc_final: 0.8150 (m-10) REVERT: I 46 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7657 (tm-30) REVERT: I 48 ILE cc_start: 0.8803 (mm) cc_final: 0.8233 (mm) REVERT: I 82 GLN cc_start: 0.7564 (tp40) cc_final: 0.6802 (tm-30) REVERT: I 90 ASP cc_start: 0.8230 (m-30) cc_final: 0.7993 (m-30) outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 0.1179 time to fit residues: 72.8815 Evaluate side-chains 315 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 chunk 71 optimal weight: 0.3980 chunk 66 optimal weight: 0.0060 chunk 67 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 GLN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 GLN L 105 ASN ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 HIS E 290 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.108295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.090399 restraints weight = 35933.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.091193 restraints weight = 24458.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.092430 restraints weight = 20124.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.093262 restraints weight = 14107.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.093404 restraints weight = 13084.040| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17463 Z= 0.116 Angle : 0.588 6.763 23727 Z= 0.307 Chirality : 0.043 0.152 2622 Planarity : 0.004 0.059 3027 Dihedral : 4.126 31.497 2319 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.05 % Allowed : 0.87 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.18), residues: 2133 helix: 1.89 (0.27), residues: 357 sheet: 1.00 (0.22), residues: 516 loop : -0.65 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 87 TYR 0.043 0.001 TYR M 94 PHE 0.027 0.002 PHE C 210 TRP 0.043 0.002 TRP J 43 HIS 0.011 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (17418) covalent geometry : angle 0.57571 / 0.30 (23616) SS BOND : bond 0.00444 / 0.29 ( 24) SS BOND : angle 1.84043 / 1.00 ( 48) hydrogen bonds : bond 0.03825 / 2.53 ( 702) hydrogen bonds : angle 5.15917 / 3.47 ( 1926) link_BETA1-4 : bond 0.00535 / 0.27 ( 3) link_BETA1-4 : angle 4.11183 / 2.03 ( 9) link_NAG-ASN : bond 0.00138 / 0.08 ( 18) link_NAG-ASN : angle 1.05466 / 0.72 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 380 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 TYR cc_start: 0.7795 (t80) cc_final: 0.7491 (t80) REVERT: A 237 MET cc_start: 0.8489 (tpp) cc_final: 0.8156 (mpp) REVERT: B 17 MET cc_start: 0.8719 (ttp) cc_final: 0.8001 (ppp) REVERT: B 135 ASN cc_start: 0.7019 (p0) cc_final: 0.6801 (p0) REVERT: M 36 TRP cc_start: 0.7856 (m100) cc_final: 0.7527 (m100) REVERT: M 47 TRP cc_start: 0.8510 (t60) cc_final: 0.8158 (t60) REVERT: M 48 ILE cc_start: 0.8822 (mm) cc_final: 0.8129 (mm) REVERT: M 82 GLN cc_start: 0.7444 (tp40) cc_final: 0.6774 (tm-30) REVERT: M 87 ARG cc_start: 0.7570 (mtm-85) cc_final: 0.7131 (mtm-85) REVERT: M 99 ASP cc_start: 0.8157 (m-30) cc_final: 0.7577 (m-30) REVERT: N 46 GLN cc_start: 0.8679 (tp40) cc_final: 0.8455 (tp40) REVERT: N 99 TRP cc_start: 0.8143 (t-100) cc_final: 0.7202 (t-100) REVERT: N 105 ASN cc_start: 0.7676 (m-40) cc_final: 0.7233 (m-40) REVERT: C 44 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7644 (mt-10) REVERT: C 108 TYR cc_start: 0.7897 (t80) cc_final: 0.7637 (t80) REVERT: C 204 ASN cc_start: 0.8846 (m-40) cc_final: 0.8453 (m-40) REVERT: H 82 GLN cc_start: 0.7269 (tm-30) cc_final: 0.6984 (tm-30) REVERT: H 83 MET cc_start: 0.7469 (mtt) cc_final: 0.7207 (mtt) REVERT: H 87 ARG cc_start: 0.7638 (mtm-85) cc_final: 0.7258 (mtm-85) REVERT: H 90 ASP cc_start: 0.8134 (m-30) cc_final: 0.7890 (m-30) REVERT: H 94 TYR cc_start: 0.7389 (m-80) cc_final: 0.7101 (m-10) REVERT: E 77 CYS cc_start: 0.5819 (m) cc_final: 0.5571 (m) REVERT: E 108 TYR cc_start: 0.7957 (t80) cc_final: 0.7720 (t80) REVERT: E 155 TYR cc_start: 0.8334 (m-80) cc_final: 0.7895 (m-80) REVERT: E 203 GLN cc_start: 0.8514 (tm-30) cc_final: 0.8128 (tm-30) REVERT: F 17 MET cc_start: 0.8675 (tmm) cc_final: 0.8329 (tmm) REVERT: F 26 HIS cc_start: 0.8388 (p90) cc_final: 0.8076 (p90) REVERT: I 32 TYR cc_start: 0.8401 (m-10) cc_final: 0.8138 (m-10) REVERT: I 34 MET cc_start: 0.7578 (mmt) cc_final: 0.7328 (mmt) REVERT: I 46 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7544 (tm-30) REVERT: I 48 ILE cc_start: 0.8779 (mm) cc_final: 0.8211 (mm) REVERT: I 82 GLN cc_start: 0.7523 (tp40) cc_final: 0.6810 (tm-30) REVERT: I 90 ASP cc_start: 0.8281 (m-30) cc_final: 0.7993 (m-30) REVERT: J 108 PHE cc_start: 0.7974 (m-80) cc_final: 0.7748 (m-10) outliers start: 1 outliers final: 0 residues processed: 380 average time/residue: 0.1142 time to fit residues: 69.5419 Evaluate side-chains 321 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 159 optimal weight: 0.8980 chunk 174 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 58 optimal weight: 0.3980 chunk 35 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 HIS A 290 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 GLN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 HIS E 290 GLN F 27 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.109088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.090460 restraints weight = 35720.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.092431 restraints weight = 24756.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.093631 restraints weight = 16756.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.094391 restraints weight = 12965.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.094573 restraints weight = 12205.299| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17463 Z= 0.129 Angle : 0.600 11.171 23727 Z= 0.312 Chirality : 0.044 0.162 2622 Planarity : 0.004 0.055 3027 Dihedral : 4.229 30.537 2319 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.11 % Allowed : 0.33 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.17), residues: 2133 helix: 1.77 (0.26), residues: 357 sheet: 1.01 (0.22), residues: 516 loop : -0.62 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 87 TYR 0.033 0.001 TYR M 94 PHE 0.029 0.002 PHE E 124 TRP 0.031 0.001 TRP N 43 HIS 0.012 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (17418) covalent geometry : angle 0.58731 / 0.31 (23616) SS BOND : bond 0.00589 / 0.45 ( 24) SS BOND : angle 1.97927 / 1.16 ( 48) hydrogen bonds : bond 0.03901 / 2.59 ( 702) hydrogen bonds : angle 5.12356 / 3.46 ( 1926) link_BETA1-4 : bond 0.00497 / 0.25 ( 3) link_BETA1-4 : angle 3.93587 / 1.95 ( 9) link_NAG-ASN : bond 0.00157 / 0.10 ( 18) link_NAG-ASN : angle 1.05586 / 0.73 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 384 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 TYR cc_start: 0.7839 (t80) cc_final: 0.7411 (t80) REVERT: A 237 MET cc_start: 0.8468 (tpp) cc_final: 0.8141 (mpp) REVERT: B 17 MET cc_start: 0.8717 (ttp) cc_final: 0.8013 (ppp) REVERT: B 105 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7868 (mm-30) REVERT: M 47 TRP cc_start: 0.8478 (t60) cc_final: 0.8045 (t60) REVERT: M 48 ILE cc_start: 0.8830 (mm) cc_final: 0.8138 (mm) REVERT: M 82 GLN cc_start: 0.7573 (tp40) cc_final: 0.6837 (tm-30) REVERT: M 87 ARG cc_start: 0.7495 (mtm-85) cc_final: 0.7052 (mtm-85) REVERT: M 90 ASP cc_start: 0.8291 (m-30) cc_final: 0.7861 (m-30) REVERT: M 99 ASP cc_start: 0.8301 (m-30) cc_final: 0.7788 (m-30) REVERT: M 112 TYR cc_start: 0.7938 (m-80) cc_final: 0.7272 (m-10) REVERT: N 99 TRP cc_start: 0.8183 (t-100) cc_final: 0.7431 (t-100) REVERT: N 105 ASN cc_start: 0.7556 (m-40) cc_final: 0.7151 (m-40) REVERT: C 44 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7648 (mt-10) REVERT: C 108 TYR cc_start: 0.7921 (t80) cc_final: 0.7606 (t80) REVERT: C 204 ASN cc_start: 0.8841 (m-40) cc_final: 0.8483 (m-40) REVERT: C 269 ARG cc_start: 0.8189 (mtm110) cc_final: 0.7894 (mtm110) REVERT: H 82 GLN cc_start: 0.7273 (tm-30) cc_final: 0.6941 (tm-30) REVERT: H 83 MET cc_start: 0.7395 (mtt) cc_final: 0.6938 (mtt) REVERT: H 87 ARG cc_start: 0.7645 (mtm-85) cc_final: 0.7192 (mtm-85) REVERT: H 90 ASP cc_start: 0.8202 (m-30) cc_final: 0.7956 (m-30) REVERT: H 94 TYR cc_start: 0.7415 (m-80) cc_final: 0.7073 (m-10) REVERT: L 43 TRP cc_start: 0.7611 (m100) cc_final: 0.7011 (m100) REVERT: E 77 CYS cc_start: 0.5745 (m) cc_final: 0.5528 (m) REVERT: E 108 TYR cc_start: 0.8129 (t80) cc_final: 0.7849 (t80) REVERT: E 203 GLN cc_start: 0.8520 (tm-30) cc_final: 0.8110 (tm-30) REVERT: F 17 MET cc_start: 0.8711 (tmm) cc_final: 0.8305 (tmm) REVERT: F 26 HIS cc_start: 0.8367 (p90) cc_final: 0.8090 (p90) REVERT: I 32 TYR cc_start: 0.8472 (m-10) cc_final: 0.8076 (m-10) REVERT: I 36 TRP cc_start: 0.8753 (m100) cc_final: 0.8494 (m100) REVERT: I 46 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7592 (tm-30) REVERT: I 48 ILE cc_start: 0.8934 (mm) cc_final: 0.8450 (mm) REVERT: I 82 GLN cc_start: 0.7555 (tp40) cc_final: 0.6778 (tm-30) REVERT: I 87 ARG cc_start: 0.7773 (mtm-85) cc_final: 0.7462 (mtm-85) REVERT: I 90 ASP cc_start: 0.8171 (m-30) cc_final: 0.7911 (m-30) outliers start: 2 outliers final: 0 residues processed: 384 average time/residue: 0.1158 time to fit residues: 70.8561 Evaluate side-chains 322 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 154 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 209 optimal weight: 0.0370 chunk 201 optimal weight: 10.0000 chunk 191 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 chunk 188 optimal weight: 8.9990 chunk 30 optimal weight: 0.0010 chunk 0 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.7466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 HIS A 290 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS C 290 GLN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 HIS E 290 GLN F 125 GLN ** J 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.109936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.091045 restraints weight = 35626.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.093339 restraints weight = 25489.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.094354 restraints weight = 17861.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.094736 restraints weight = 13267.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.094995 restraints weight = 12382.426| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17463 Z= 0.126 Angle : 0.616 13.408 23727 Z= 0.320 Chirality : 0.044 0.184 2622 Planarity : 0.004 0.052 3027 Dihedral : 4.242 32.238 2319 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.11 % Allowed : 0.22 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.17), residues: 2133 helix: 1.60 (0.26), residues: 357 sheet: 1.01 (0.22), residues: 516 loop : -0.61 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 61 TYR 0.045 0.001 TYR M 94 PHE 0.027 0.002 PHE E 124 TRP 0.038 0.002 TRP E 241 HIS 0.004 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (17418) covalent geometry : angle 0.60472 / 0.32 (23616) SS BOND : bond 0.00549 / 0.41 ( 24) SS BOND : angle 1.92852 / 1.14 ( 48) hydrogen bonds : bond 0.04009 / 2.66 ( 702) hydrogen bonds : angle 5.17357 / 3.50 ( 1926) link_BETA1-4 : bond 0.00523 / 0.26 ( 3) link_BETA1-4 : angle 3.86683 / 1.91 ( 9) link_NAG-ASN : bond 0.00137 / 0.08 ( 18) link_NAG-ASN : angle 1.05560 / 0.72 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 367 time to evaluate : 0.663 Fit side-chains revert: symmetry clash REVERT: A 108 TYR cc_start: 0.7805 (t80) cc_final: 0.7496 (t80) REVERT: A 237 MET cc_start: 0.8468 (tpp) cc_final: 0.8126 (mpp) REVERT: B 17 MET cc_start: 0.8697 (ttp) cc_final: 0.8016 (ppp) REVERT: M 36 TRP cc_start: 0.8483 (m100) cc_final: 0.8232 (m100) REVERT: M 47 TRP cc_start: 0.8408 (t60) cc_final: 0.7964 (t60) REVERT: M 48 ILE cc_start: 0.8755 (mm) cc_final: 0.8094 (mm) REVERT: M 82 GLN cc_start: 0.7588 (tp40) cc_final: 0.6843 (tm-30) REVERT: M 87 ARG cc_start: 0.7567 (mtm-85) cc_final: 0.7119 (mtm-85) REVERT: M 90 ASP cc_start: 0.8291 (m-30) cc_final: 0.7781 (m-30) REVERT: M 99 ASP cc_start: 0.8165 (m-30) cc_final: 0.7497 (m-30) REVERT: M 112 TYR cc_start: 0.7955 (m-80) cc_final: 0.7243 (m-10) REVERT: N 99 TRP cc_start: 0.8213 (t-100) cc_final: 0.7452 (t-100) REVERT: N 105 ASN cc_start: 0.7638 (m-40) cc_final: 0.7218 (m-40) REVERT: C 44 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7645 (mt-10) REVERT: C 108 TYR cc_start: 0.7848 (t80) cc_final: 0.7523 (t80) REVERT: C 204 ASN cc_start: 0.8828 (m-40) cc_final: 0.8488 (m-40) REVERT: C 270 ASN cc_start: 0.7424 (t0) cc_final: 0.6991 (t0) REVERT: D 105 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7536 (mm-30) REVERT: H 36 TRP cc_start: 0.8661 (m100) cc_final: 0.8111 (m100) REVERT: H 83 MET cc_start: 0.7350 (mtt) cc_final: 0.7003 (mtt) REVERT: H 90 ASP cc_start: 0.8209 (m-30) cc_final: 0.7943 (m-30) REVERT: H 94 TYR cc_start: 0.7497 (m-80) cc_final: 0.7176 (m-10) REVERT: L 43 TRP cc_start: 0.7775 (m100) cc_final: 0.6806 (m100) REVERT: E 77 CYS cc_start: 0.5760 (m) cc_final: 0.5546 (m) REVERT: E 108 TYR cc_start: 0.8048 (t80) cc_final: 0.7666 (t80) REVERT: F 17 MET cc_start: 0.8653 (tmm) cc_final: 0.8283 (tmm) REVERT: F 26 HIS cc_start: 0.8348 (p90) cc_final: 0.8041 (p90) REVERT: I 32 TYR cc_start: 0.8402 (m-10) cc_final: 0.8173 (m-10) REVERT: I 46 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7592 (tm-30) REVERT: I 48 ILE cc_start: 0.8951 (mm) cc_final: 0.8411 (mm) REVERT: I 82 GLN cc_start: 0.7501 (tp40) cc_final: 0.6768 (tm-30) REVERT: I 87 ARG cc_start: 0.7775 (mtm-85) cc_final: 0.7399 (mtm-85) REVERT: I 90 ASP cc_start: 0.8170 (m-30) cc_final: 0.7900 (m-30) outliers start: 2 outliers final: 0 residues processed: 367 average time/residue: 0.1141 time to fit residues: 67.4683 Evaluate side-chains 303 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 3 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 157 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 chunk 144 optimal weight: 0.3980 chunk 104 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 135 optimal weight: 0.0370 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN C 290 GLN D 60 ASN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 HIS E 290 GLN F 125 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.110300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.091594 restraints weight = 35771.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.093712 restraints weight = 24872.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.094931 restraints weight = 16609.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.095343 restraints weight = 12638.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.095595 restraints weight = 12284.684| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17463 Z= 0.119 Angle : 0.603 9.298 23727 Z= 0.314 Chirality : 0.044 0.194 2622 Planarity : 0.004 0.046 3027 Dihedral : 4.208 30.986 2319 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.05 % Allowed : 0.38 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.17), residues: 2133 helix: 1.72 (0.26), residues: 357 sheet: 1.01 (0.22), residues: 516 loop : -0.61 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 61 TYR 0.019 0.001 TYR B 110 PHE 0.026 0.002 PHE A 124 TRP 0.038 0.002 TRP E 241 HIS 0.005 0.001 HIS M 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (17418) covalent geometry : angle 0.59251 / 0.31 (23616) SS BOND : bond 0.00520 / 0.38 ( 24) SS BOND : angle 1.80594 / 1.07 ( 48) hydrogen bonds : bond 0.03912 / 2.60 ( 702) hydrogen bonds : angle 5.13033 / 3.48 ( 1926) link_BETA1-4 : bond 0.00417 / 0.21 ( 3) link_BETA1-4 : angle 3.74290 / 1.86 ( 9) link_NAG-ASN : bond 0.00148 / 0.09 ( 18) link_NAG-ASN : angle 1.03744 / 0.70 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2789.65 seconds wall clock time: 49 minutes 23.35 seconds (2963.35 seconds total)