Starting phenix.real_space_refine on Thu Jul 2 11:16:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9muo_48639/07_2026/9muo_48639.cif Found real_map, /net/cci-nas-00/data/ceres_data/9muo_48639/07_2026/9muo_48639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9muo_48639/07_2026/9muo_48639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9muo_48639/07_2026/9muo_48639.map" model { file = "/net/cci-nas-00/data/ceres_data/9muo_48639/07_2026/9muo_48639.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9muo_48639/07_2026/9muo_48639.cif" } resolution = 3.3 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= 0.002 sd= 0.013 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: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 20 5.16 5 C 5426 2.51 5 N 1426 2.21 5 O 1528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8410 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2022 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain breaks: 1 Chain: "a" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 4} Link IDs: {'rna2p': 3} Chain: "b" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 4} Link IDs: {'rna2p': 3} Chain: "B" Number of atoms: 2073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2073 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 13, 'TRANS': 243} Chain: "C" Number of atoms: 2022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2022 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 12, 'TRANS': 236} Chain breaks: 1 Chain: "D" Number of atoms: 2073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2073 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 13, 'TRANS': 243} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'DQV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.78, per 1000 atoms: 0.21 Number of scatterers: 8410 At special positions: 0 Unit cell: (82.65, 131.225, 83.375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 10 15.00 O 1528 8.00 N 1426 7.00 C 5426 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 271.5 milliseconds 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1932 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 8 sheets defined 39.9% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 9 through 11 No H-bonds generated for 'chain 'A' and resid 9 through 11' Processing helix chain 'A' and resid 12 through 25 removed outlier: 3.743A pdb=" N LEU A 17 " --> pdb=" O LYS A 13 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU A 18 " --> pdb=" O LYS A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 67 Processing helix chain 'A' and resid 68 through 81 removed outlier: 4.764A pdb=" N GLU A 74 " --> pdb=" O TRP A 70 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A 75 " --> pdb=" O CYS A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 85 Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 106 through 119 Processing helix chain 'A' and resid 129 through 144 removed outlier: 4.631A pdb=" N ASN A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 removed outlier: 3.985A pdb=" N HIS A 181 " --> pdb=" O ASP A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 removed outlier: 3.657A pdb=" N ASP A 188 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE A 190 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 222 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'B' and resid 9 through 11 No H-bonds generated for 'chain 'B' and resid 9 through 11' Processing helix chain 'B' and resid 12 through 25 removed outlier: 3.743A pdb=" N LEU B 17 " --> pdb=" O LYS B 13 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU B 18 " --> pdb=" O LYS B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 67 Processing helix chain 'B' and resid 68 through 81 removed outlier: 4.591A pdb=" N GLU B 74 " --> pdb=" O TRP B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 85 Processing helix chain 'B' and resid 96 through 100 Processing helix chain 'B' and resid 106 through 119 Processing helix chain 'B' and resid 129 through 144 removed outlier: 4.631A pdb=" N ASN B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 182 removed outlier: 3.984A pdb=" N HIS B 181 " --> pdb=" O ASP B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 190 removed outlier: 3.657A pdb=" N ASP B 188 " --> pdb=" O LYS B 185 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE B 190 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 222 Processing helix chain 'B' and resid 223 through 225 No H-bonds generated for 'chain 'B' and resid 223 through 225' Processing helix chain 'C' and resid 9 through 11 No H-bonds generated for 'chain 'C' and resid 9 through 11' Processing helix chain 'C' and resid 12 through 25 removed outlier: 3.743A pdb=" N LEU C 17 " --> pdb=" O LYS C 13 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU C 18 " --> pdb=" O LYS C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 67 Processing helix chain 'C' and resid 68 through 81 removed outlier: 4.763A pdb=" N GLU C 74 " --> pdb=" O TRP C 70 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU C 75 " --> pdb=" O CYS C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 85 Processing helix chain 'C' and resid 96 through 100 Processing helix chain 'C' and resid 106 through 119 Processing helix chain 'C' and resid 129 through 144 removed outlier: 4.631A pdb=" N ASN C 144 " --> pdb=" O ALA C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 182 removed outlier: 3.985A pdb=" N HIS C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 190 removed outlier: 3.657A pdb=" N ASP C 188 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE C 190 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 222 Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'D' and resid 9 through 11 No H-bonds generated for 'chain 'D' and resid 9 through 11' Processing helix chain 'D' and resid 12 through 25 removed outlier: 3.742A pdb=" N LEU D 17 " --> pdb=" O LYS D 13 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU D 18 " --> pdb=" O LYS D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 67 Processing helix chain 'D' and resid 68 through 81 removed outlier: 4.763A pdb=" N GLU D 74 " --> pdb=" O TRP D 70 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU D 75 " --> pdb=" O CYS D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 85 Processing helix chain 'D' and resid 96 through 100 Processing helix chain 'D' and resid 106 through 119 Processing helix chain 'D' and resid 129 through 144 removed outlier: 4.631A pdb=" N ASN D 144 " --> pdb=" O ALA D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 182 removed outlier: 3.984A pdb=" N HIS D 181 " --> pdb=" O ASP D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 190 removed outlier: 3.656A pdb=" N ASP D 188 " --> pdb=" O LYS D 185 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE D 190 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 222 Processing helix chain 'D' and resid 223 through 225 No H-bonds generated for 'chain 'D' and resid 223 through 225' Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 31 removed outlier: 6.207A pdb=" N ALA A 4 " --> pdb=" O TRP A 31 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N GLN A 3 " --> pdb=" O TYR A 56 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU A 58 " --> pdb=" O GLN A 3 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N PHE A 5 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N PHE A 60 " --> pdb=" O PHE A 5 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N SER A 7 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLN A 55 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE A 90 " --> pdb=" O GLN A 55 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N PHE A 57 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE A 92 " --> pdb=" O PHE A 57 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ALA A 59 " --> pdb=" O ILE A 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 153 through 157 removed outlier: 6.532A pdb=" N VAL A 206 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N PHE A 233 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU A 208 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 239 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR A 240 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 30 through 31 removed outlier: 6.380A pdb=" N ALA B 4 " --> pdb=" O TRP B 31 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N GLN B 3 " --> pdb=" O TYR B 56 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N LEU B 58 " --> pdb=" O GLN B 3 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N PHE B 5 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N PHE B 60 " --> pdb=" O PHE B 5 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N SER B 7 " --> pdb=" O PHE B 60 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLN B 55 " --> pdb=" O LYS B 88 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE B 90 " --> pdb=" O GLN B 55 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N PHE B 57 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE B 92 " --> pdb=" O PHE B 57 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ALA B 59 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 153 through 157 removed outlier: 6.532A pdb=" N VAL B 206 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N PHE B 233 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU B 208 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU B 239 " --> pdb=" O ASN B 234 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR B 240 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 30 through 31 removed outlier: 6.208A pdb=" N ALA C 4 " --> pdb=" O TRP C 31 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N GLN C 3 " --> pdb=" O TYR C 56 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU C 58 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N PHE C 5 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N PHE C 60 " --> pdb=" O PHE C 5 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N SER C 7 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLN C 55 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE C 90 " --> pdb=" O GLN C 55 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N PHE C 57 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE C 92 " --> pdb=" O PHE C 57 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ALA C 59 " --> pdb=" O ILE C 92 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 153 through 157 removed outlier: 6.532A pdb=" N VAL C 206 " --> pdb=" O PHE C 231 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N PHE C 233 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU C 208 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU C 239 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR C 240 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 30 through 31 removed outlier: 6.208A pdb=" N ALA D 4 " --> pdb=" O TRP D 31 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N GLN D 3 " --> pdb=" O TYR D 56 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N LEU D 58 " --> pdb=" O GLN D 3 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE D 5 " --> pdb=" O LEU D 58 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N PHE D 60 " --> pdb=" O PHE D 5 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N SER D 7 " --> pdb=" O PHE D 60 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLN D 55 " --> pdb=" O LYS D 88 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE D 90 " --> pdb=" O GLN D 55 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N PHE D 57 " --> pdb=" O ILE D 90 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE D 92 " --> pdb=" O PHE D 57 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ALA D 59 " --> pdb=" O ILE D 92 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 153 through 157 removed outlier: 6.532A pdb=" N VAL D 206 " --> pdb=" O PHE D 231 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N PHE D 233 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU D 208 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU D 239 " --> pdb=" O ASN D 234 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR D 240 " --> pdb=" O LEU D 256 " (cutoff:3.500A) 261 hydrogen bonds defined for protein. 699 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: 0.92 Time building geometry restraints manager: 0.83 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: 2546 1.34 - 1.45: 1373 1.45 - 1.57: 4675 1.57 - 1.69: 22 1.69 - 1.81: 32 Bond restraints: 8648 Sorted by residual: bond pdb=" N GLN B 35 " pdb=" CA GLN B 35 " ideal model delta sigma weight residual 1.452 1.487 -0.035 1.25e-02 6.40e+03 7.74e+00 bond pdb=" N ILE B 32 " pdb=" CA ILE B 32 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 6.91e+00 bond pdb=" N ASP B 33 " pdb=" CA ASP B 33 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.25e-02 6.40e+03 6.73e+00 bond pdb=" N ILE B 37 " pdb=" CA ILE B 37 " ideal model delta sigma weight residual 1.461 1.493 -0.031 1.23e-02 6.61e+03 6.54e+00 bond pdb=" N ILE B 44 " pdb=" CA ILE B 44 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.25e-02 6.40e+03 6.39e+00 ... (remaining 8643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 11633 3.02 - 6.04: 127 6.04 - 9.05: 18 9.05 - 12.07: 4 12.07 - 15.09: 1 Bond angle restraints: 11783 Sorted by residual: angle pdb=" CA PRO C 170 " pdb=" N PRO C 170 " pdb=" CD PRO C 170 " ideal model delta sigma weight residual 112.00 104.37 7.63 1.40e+00 5.10e-01 2.97e+01 angle pdb=" CA PRO D 170 " pdb=" N PRO D 170 " pdb=" CD PRO D 170 " ideal model delta sigma weight residual 112.00 104.39 7.61 1.40e+00 5.10e-01 2.96e+01 angle pdb=" CA PRO A 170 " pdb=" N PRO A 170 " pdb=" CD PRO A 170 " ideal model delta sigma weight residual 112.00 104.39 7.61 1.40e+00 5.10e-01 2.96e+01 angle pdb=" CA PRO B 170 " pdb=" N PRO B 170 " pdb=" CD PRO B 170 " ideal model delta sigma weight residual 112.00 104.42 7.58 1.40e+00 5.10e-01 2.93e+01 angle pdb=" P DQV B 301 " pdb=" O5 DQV B 301 " pdb=" P1 DQV B 301 " ideal model delta sigma weight residual 124.76 139.85 -15.09 3.00e+00 1.11e-01 2.53e+01 ... (remaining 11778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4336 17.98 - 35.96: 629 35.96 - 53.94: 153 53.94 - 71.91: 21 71.91 - 89.89: 12 Dihedral angle restraints: 5151 sinusoidal: 2181 harmonic: 2970 Sorted by residual: dihedral pdb=" CD ARG D 119 " pdb=" NE ARG D 119 " pdb=" CZ ARG D 119 " pdb=" NH1 ARG D 119 " ideal model delta sinusoidal sigma weight residual 0.00 50.44 -50.44 1 1.00e+01 1.00e-02 3.49e+01 dihedral pdb=" CA ASP D 33 " pdb=" C ASP D 33 " pdb=" N GLN D 34 " pdb=" CA GLN D 34 " ideal model delta harmonic sigma weight residual 180.00 157.01 22.99 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA SER C 238 " pdb=" C SER C 238 " pdb=" N GLU C 239 " pdb=" CA GLU C 239 " ideal model delta harmonic sigma weight residual 180.00 159.44 20.56 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 5148 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1036 0.051 - 0.103: 202 0.103 - 0.154: 70 0.154 - 0.205: 3 0.205 - 0.256: 1 Chirality restraints: 1312 Sorted by residual: chirality pdb=" C20 DQV B 301 " pdb=" C21 DQV B 301 " pdb=" C8 DQV B 301 " pdb=" O12 DQV B 301 " both_signs ideal model delta sigma weight residual False -2.55 -2.81 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" C21 DQV B 301 " pdb=" C20 DQV B 301 " pdb=" C7 DQV B 301 " pdb=" O13 DQV B 301 " both_signs ideal model delta sigma weight residual False 2.73 2.54 0.19 2.00e-01 2.50e+01 9.23e-01 chirality pdb=" CA ILE B 32 " pdb=" N ILE B 32 " pdb=" C ILE B 32 " pdb=" CB ILE B 32 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.10e-01 ... (remaining 1309 not shown) Planarity restraints: 1459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 119 " -0.839 9.50e-02 1.11e+02 3.76e-01 8.60e+01 pdb=" NE ARG D 119 " 0.050 2.00e-02 2.50e+03 pdb=" CZ ARG D 119 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG D 119 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 119 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 169 " -0.068 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO D 170 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO D 170 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO D 170 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 169 " -0.068 5.00e-02 4.00e+02 9.80e-02 1.54e+01 pdb=" N PRO B 170 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO B 170 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 170 " -0.053 5.00e-02 4.00e+02 ... (remaining 1456 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1038 2.75 - 3.29: 8577 3.29 - 3.83: 14337 3.83 - 4.36: 17326 4.36 - 4.90: 28583 Nonbonded interactions: 69861 Sorted by model distance: nonbonded pdb=" N GLN B 99 " pdb=" OE1 GLN B 99 " model vdw 2.216 3.120 nonbonded pdb=" N GLN C 99 " pdb=" OE1 GLN C 99 " model vdw 2.216 3.120 nonbonded pdb=" N GLN A 99 " pdb=" OE1 GLN A 99 " model vdw 2.217 3.120 nonbonded pdb=" N GLN D 99 " pdb=" OE1 GLN D 99 " model vdw 2.217 3.120 nonbonded pdb=" OH TYR C 56 " pdb=" OE1 GLU C 145 " model vdw 2.266 3.040 ... (remaining 69856 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 2 through 33 or resid 42 through 258)) selection = chain 'C' selection = (chain 'D' and (resid 2 through 33 or resid 42 through 258)) } ncs_group { reference = chain 'a' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.650 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.070 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 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 : 0.005 0.109 8648 Z= 0.217 Angle : 0.814 15.087 11783 Z= 0.433 Chirality : 0.046 0.256 1312 Planarity : 0.012 0.376 1459 Dihedral : 17.637 89.893 3219 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.30 % Favored : 94.30 % Rotamer: Outliers : 1.45 % Allowed : 31.74 % Favored : 66.82 % 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: -0.28 (0.28), residues: 1000 helix: -0.12 (0.31), residues: 312 sheet: -0.37 (0.40), residues: 192 loop : 0.03 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 148 TYR 0.015 0.001 TYR D 122 PHE 0.015 0.001 PHE C 6 TRP 0.012 0.001 TRP C 31 HIS 0.001 0.000 HIS C 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.22 ( 8648) covalent geometry : angle 0.81399 / 0.43 (11783) hydrogen bonds : bond 0.30607 / 20.04 ( 261) hydrogen bonds : angle 8.36780 / 5.92 ( 699) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 258 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8268 (pm20) cc_final: 0.7988 (pm20) REVERT: B 68 SER cc_start: 0.8876 (OUTLIER) cc_final: 0.8462 (t) REVERT: B 101 ASP cc_start: 0.8619 (t0) cc_final: 0.8415 (t0) REVERT: C 3 GLN cc_start: 0.7851 (mp10) cc_final: 0.7506 (mp10) REVERT: C 11 LYS cc_start: 0.9337 (mmtm) cc_final: 0.9119 (mttp) REVERT: C 129 ASN cc_start: 0.8386 (t0) cc_final: 0.7979 (t0) REVERT: C 142 TRP cc_start: 0.9061 (m100) cc_final: 0.8761 (m100) REVERT: C 143 GLN cc_start: 0.8997 (tt0) cc_final: 0.8324 (tm-30) REVERT: C 144 ASN cc_start: 0.8734 (p0) cc_final: 0.8468 (p0) REVERT: C 183 ASP cc_start: 0.8462 (p0) cc_final: 0.8037 (p0) REVERT: C 195 ASN cc_start: 0.9141 (m-40) cc_final: 0.8833 (p0) REVERT: C 209 TYR cc_start: 0.8651 (t80) cc_final: 0.8030 (t80) REVERT: D 24 ARG cc_start: 0.8428 (ttp80) cc_final: 0.7814 (ttp80) REVERT: D 34 GLN cc_start: 0.4719 (OUTLIER) cc_final: 0.1972 (pp30) REVERT: D 101 ASP cc_start: 0.8694 (t0) cc_final: 0.7914 (p0) REVERT: D 114 GLU cc_start: 0.9280 (tp30) cc_final: 0.9077 (mm-30) REVERT: D 122 TYR cc_start: 0.8456 (p90) cc_final: 0.8017 (p90) REVERT: D 132 ARG cc_start: 0.8717 (tmt170) cc_final: 0.8397 (tmm-80) REVERT: D 166 GLU cc_start: 0.8943 (tp30) cc_final: 0.8703 (tp30) REVERT: D 185 LYS cc_start: 0.8981 (ptpp) cc_final: 0.8687 (pttm) outliers start: 13 outliers final: 2 residues processed: 264 average time/residue: 0.0816 time to fit residues: 29.1590 Evaluate side-chains 186 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 182 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain D residue 34 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 20.0000 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.0010 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.0770 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.2346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 46 GLN D 234 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.098740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.071385 restraints weight = 19012.279| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.68 r_work: 0.3006 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8648 Z= 0.162 Angle : 0.708 7.759 11783 Z= 0.364 Chirality : 0.049 0.194 1312 Planarity : 0.006 0.054 1459 Dihedral : 10.556 77.281 1226 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.23 % Allowed : 29.40 % Favored : 67.37 % 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: -0.10 (0.27), residues: 1000 helix: 0.02 (0.29), residues: 324 sheet: -0.31 (0.35), residues: 224 loop : 0.22 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 148 TYR 0.023 0.002 TYR A 79 PHE 0.011 0.001 PHE C 60 TRP 0.019 0.001 TRP B 31 HIS 0.002 0.001 HIS A 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 8648) covalent geometry : angle 0.70824 / 0.36 (11783) hydrogen bonds : bond 0.06768 / 4.33 ( 261) hydrogen bonds : angle 5.83353 / 4.11 ( 699) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8924 (pm20) cc_final: 0.8706 (pm20) REVERT: A 79 TYR cc_start: 0.9514 (t80) cc_final: 0.9304 (t80) REVERT: A 95 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7956 (t) REVERT: A 101 ASP cc_start: 0.9001 (t0) cc_final: 0.8791 (t0) REVERT: A 143 GLN cc_start: 0.8974 (tm-30) cc_final: 0.8691 (tm-30) REVERT: A 166 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8182 (tt0) REVERT: A 185 LYS cc_start: 0.9231 (ptpp) cc_final: 0.8830 (ptmt) REVERT: B 119 ARG cc_start: 0.8753 (ttp-110) cc_final: 0.8545 (ptp-110) REVERT: C 11 LYS cc_start: 0.9436 (mmtm) cc_final: 0.9060 (mttp) REVERT: C 129 ASN cc_start: 0.8512 (t0) cc_final: 0.7986 (t0) REVERT: C 142 TRP cc_start: 0.9021 (m100) cc_final: 0.8816 (m100) REVERT: C 143 GLN cc_start: 0.9186 (tt0) cc_final: 0.8461 (tm-30) REVERT: C 144 ASN cc_start: 0.8830 (p0) cc_final: 0.8518 (p0) REVERT: C 195 ASN cc_start: 0.9374 (m-40) cc_final: 0.9015 (p0) REVERT: C 209 TYR cc_start: 0.8743 (t80) cc_final: 0.7981 (t80) REVERT: D 97 ARG cc_start: 0.8732 (tpt-90) cc_final: 0.8434 (ttt180) REVERT: D 101 ASP cc_start: 0.8755 (t0) cc_final: 0.7949 (p0) REVERT: D 119 ARG cc_start: 0.9387 (ptp90) cc_final: 0.9185 (ptp90) REVERT: D 132 ARG cc_start: 0.8983 (tmt170) cc_final: 0.8619 (tmm-80) REVERT: D 154 MET cc_start: 0.9075 (mtp) cc_final: 0.8470 (mtp) REVERT: D 161 GLU cc_start: 0.8784 (tp30) cc_final: 0.8269 (tp30) outliers start: 29 outliers final: 19 residues processed: 213 average time/residue: 0.0848 time to fit residues: 24.4900 Evaluate side-chains 194 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 188 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 ASN B 226 ASN B 234 ASN C 234 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.092424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.064967 restraints weight = 19277.437| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.51 r_work: 0.2859 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 8648 Z= 0.244 Angle : 0.691 7.675 11783 Z= 0.349 Chirality : 0.048 0.174 1312 Planarity : 0.005 0.050 1459 Dihedral : 10.003 78.419 1221 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 5.23 % Allowed : 26.61 % Favored : 68.15 % 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: -0.18 (0.28), residues: 1000 helix: 0.06 (0.29), residues: 326 sheet: -0.51 (0.35), residues: 232 loop : 0.21 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 148 TYR 0.024 0.002 TYR C 244 PHE 0.021 0.002 PHE C 112 TRP 0.015 0.001 TRP B 31 HIS 0.007 0.001 HIS D 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.24 ( 8648) covalent geometry : angle 0.69132 / 0.35 (11783) hydrogen bonds : bond 0.05143 / 3.34 ( 261) hydrogen bonds : angle 5.27156 / 3.72 ( 699) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 177 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ASP cc_start: 0.9043 (t0) cc_final: 0.8745 (t0) REVERT: A 119 ARG cc_start: 0.9258 (ttp-110) cc_final: 0.8597 (ptp90) REVERT: A 166 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8223 (tp30) REVERT: A 185 LYS cc_start: 0.9246 (ptpp) cc_final: 0.8833 (ptmt) REVERT: B 119 ARG cc_start: 0.8923 (ttp-110) cc_final: 0.8709 (ptp-110) REVERT: B 166 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8599 (tp30) REVERT: C 11 LYS cc_start: 0.9466 (mmtm) cc_final: 0.9066 (mttp) REVERT: C 70 TRP cc_start: 0.8216 (OUTLIER) cc_final: 0.7755 (p-90) REVERT: C 71 CYS cc_start: 0.7582 (m) cc_final: 0.6978 (m) REVERT: C 97 ARG cc_start: 0.9166 (ttt180) cc_final: 0.8956 (tpt-90) REVERT: C 119 ARG cc_start: 0.9231 (ptp90) cc_final: 0.8940 (ptp90) REVERT: C 122 TYR cc_start: 0.8845 (p90) cc_final: 0.8512 (p90) REVERT: C 129 ASN cc_start: 0.8404 (t0) cc_final: 0.7807 (t0) REVERT: C 130 MET cc_start: 0.8661 (tpt) cc_final: 0.8319 (tpp) REVERT: C 142 TRP cc_start: 0.9124 (m100) cc_final: 0.8279 (m100) REVERT: C 166 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8379 (tp30) REVERT: C 183 ASP cc_start: 0.8928 (p0) cc_final: 0.8525 (p0) REVERT: C 195 ASN cc_start: 0.9469 (m-40) cc_final: 0.9122 (p0) REVERT: C 209 TYR cc_start: 0.8899 (t80) cc_final: 0.7892 (t80) REVERT: D 97 ARG cc_start: 0.8807 (tpt-90) cc_final: 0.8518 (ttt180) REVERT: D 101 ASP cc_start: 0.8838 (t0) cc_final: 0.7961 (p0) REVERT: D 119 ARG cc_start: 0.9432 (ptp90) cc_final: 0.9123 (ptp90) REVERT: D 132 ARG cc_start: 0.8969 (tmt170) cc_final: 0.8757 (ttp-170) REVERT: D 154 MET cc_start: 0.9190 (mtp) cc_final: 0.8515 (mtp) outliers start: 47 outliers final: 28 residues processed: 211 average time/residue: 0.0825 time to fit residues: 23.5433 Evaluate side-chains 189 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 70 TRP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 71 CYS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 166 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 89 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.089179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.062100 restraints weight = 19503.554| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 3.43 r_work: 0.2799 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 8648 Z= 0.258 Angle : 0.692 8.114 11783 Z= 0.350 Chirality : 0.049 0.193 1312 Planarity : 0.005 0.056 1459 Dihedral : 9.820 78.761 1221 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 6.12 % Allowed : 25.28 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.28), residues: 1000 helix: 0.32 (0.30), residues: 328 sheet: -0.76 (0.35), residues: 236 loop : 0.24 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 148 TYR 0.024 0.002 TYR C 244 PHE 0.026 0.002 PHE C 57 TRP 0.015 0.002 TRP B 31 HIS 0.005 0.001 HIS A 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.26 ( 8648) covalent geometry : angle 0.69238 / 0.35 (11783) hydrogen bonds : bond 0.04434 / 2.85 ( 261) hydrogen bonds : angle 5.05300 / 3.54 ( 699) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 162 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.9215 (mmtt) cc_final: 0.8882 (mttp) REVERT: A 18 GLU cc_start: 0.8657 (pp20) cc_final: 0.8449 (pp20) REVERT: A 79 TYR cc_start: 0.9488 (t80) cc_final: 0.8909 (t80) REVERT: A 117 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8905 (pp) REVERT: A 119 ARG cc_start: 0.9184 (ttp-110) cc_final: 0.8516 (ptp90) REVERT: A 166 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8328 (tp30) REVERT: A 185 LYS cc_start: 0.9257 (ptpp) cc_final: 0.8869 (ptmt) REVERT: B 166 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8566 (tp30) REVERT: C 11 LYS cc_start: 0.9497 (mmtm) cc_final: 0.9088 (mttp) REVERT: C 70 TRP cc_start: 0.8148 (OUTLIER) cc_final: 0.7397 (p-90) REVERT: C 71 CYS cc_start: 0.7833 (m) cc_final: 0.7100 (m) REVERT: C 129 ASN cc_start: 0.8427 (t0) cc_final: 0.7888 (t0) REVERT: C 166 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8435 (tp30) REVERT: C 195 ASN cc_start: 0.9477 (m-40) cc_final: 0.9111 (p0) REVERT: C 209 TYR cc_start: 0.8924 (t80) cc_final: 0.7984 (t80) REVERT: C 257 LYS cc_start: 0.6378 (tptt) cc_final: 0.6123 (tmtt) REVERT: D 101 ASP cc_start: 0.8890 (t0) cc_final: 0.8005 (p0) REVERT: D 132 ARG cc_start: 0.8943 (tmt170) cc_final: 0.8624 (tmm-80) REVERT: D 154 MET cc_start: 0.9237 (mtp) cc_final: 0.8707 (mtp) outliers start: 55 outliers final: 33 residues processed: 198 average time/residue: 0.0841 time to fit residues: 22.5364 Evaluate side-chains 188 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 70 TRP Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 204 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 27 optimal weight: 20.0000 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 0.0370 chunk 51 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 overall best weight: 4.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.088586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.061137 restraints weight = 19388.013| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 3.52 r_work: 0.2769 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 8648 Z= 0.235 Angle : 0.663 8.690 11783 Z= 0.333 Chirality : 0.047 0.142 1312 Planarity : 0.005 0.050 1459 Dihedral : 9.713 79.707 1221 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 5.79 % Allowed : 25.72 % Favored : 68.49 % 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: -0.12 (0.28), residues: 1000 helix: 0.37 (0.30), residues: 328 sheet: -0.83 (0.35), residues: 236 loop : 0.25 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 109 TYR 0.023 0.002 TYR C 122 PHE 0.015 0.001 PHE C 112 TRP 0.012 0.001 TRP C 70 HIS 0.003 0.001 HIS D 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.24 ( 8648) covalent geometry : angle 0.66262 / 0.33 (11783) hydrogen bonds : bond 0.04096 / 2.64 ( 261) hydrogen bonds : angle 4.98316 / 3.50 ( 699) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 158 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.9486 (t80) cc_final: 0.9267 (t80) REVERT: A 101 ASP cc_start: 0.9020 (t0) cc_final: 0.8678 (t0) REVERT: A 119 ARG cc_start: 0.9169 (ttp-110) cc_final: 0.8430 (ptp90) REVERT: A 166 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8327 (tp30) REVERT: A 185 LYS cc_start: 0.9227 (ptpp) cc_final: 0.8784 (ptmt) REVERT: B 97 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7139 (tpt-90) REVERT: B 166 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8550 (tp30) REVERT: C 11 LYS cc_start: 0.9488 (mmtm) cc_final: 0.9071 (mttp) REVERT: C 70 TRP cc_start: 0.8168 (OUTLIER) cc_final: 0.7305 (p-90) REVERT: C 71 CYS cc_start: 0.7759 (m) cc_final: 0.7083 (m) REVERT: C 97 ARG cc_start: 0.9177 (ttt180) cc_final: 0.8793 (ttt180) REVERT: C 109 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8671 (mmm-85) REVERT: C 119 ARG cc_start: 0.9179 (ptp90) cc_final: 0.8880 (ptp90) REVERT: C 122 TYR cc_start: 0.8814 (p90) cc_final: 0.8564 (p90) REVERT: C 129 ASN cc_start: 0.8482 (t0) cc_final: 0.7914 (t0) REVERT: C 130 MET cc_start: 0.8539 (tpt) cc_final: 0.8261 (tpp) REVERT: C 161 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8368 (tp30) REVERT: C 185 LYS cc_start: 0.9421 (ptpp) cc_final: 0.9073 (mmtm) REVERT: C 195 ASN cc_start: 0.9465 (m-40) cc_final: 0.9081 (p0) REVERT: C 257 LYS cc_start: 0.6384 (tptt) cc_final: 0.6172 (tmtt) REVERT: D 101 ASP cc_start: 0.8886 (t0) cc_final: 0.7966 (p0) REVERT: D 121 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7910 (tttt) REVERT: D 132 ARG cc_start: 0.8944 (tmt170) cc_final: 0.8616 (tmm-80) REVERT: D 154 MET cc_start: 0.9256 (mtp) cc_final: 0.8633 (mtp) outliers start: 52 outliers final: 37 residues processed: 198 average time/residue: 0.0978 time to fit residues: 25.9709 Evaluate side-chains 181 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 138 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 70 TRP Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 71 CYS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 206 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 4 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 87 optimal weight: 0.4980 chunk 52 optimal weight: 0.3980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN B 22 HIS ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.089697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.062664 restraints weight = 19176.724| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.48 r_work: 0.2794 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8648 Z= 0.159 Angle : 0.641 8.255 11783 Z= 0.322 Chirality : 0.046 0.159 1312 Planarity : 0.005 0.051 1459 Dihedral : 9.559 81.426 1221 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.01 % Allowed : 27.39 % Favored : 67.59 % 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: 0.00 (0.28), residues: 1000 helix: 0.52 (0.31), residues: 328 sheet: -0.91 (0.35), residues: 236 loop : 0.38 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 148 TYR 0.022 0.002 TYR C 122 PHE 0.014 0.001 PHE C 112 TRP 0.014 0.001 TRP C 72 HIS 0.003 0.001 HIS B 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 ( 8648) covalent geometry : angle 0.64067 / 0.32 (11783) hydrogen bonds : bond 0.03826 / 2.45 ( 261) hydrogen bonds : angle 4.83699 / 3.40 ( 699) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 154 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.9233 (mmtt) cc_final: 0.8965 (mptt) REVERT: A 119 ARG cc_start: 0.9130 (ttp-110) cc_final: 0.8372 (ptp90) REVERT: A 122 TYR cc_start: 0.8556 (p90) cc_final: 0.8189 (p90) REVERT: A 166 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8276 (tp30) REVERT: A 185 LYS cc_start: 0.9202 (ptpp) cc_final: 0.8745 (ptmt) REVERT: A 239 GLU cc_start: 0.8629 (mt-10) cc_final: 0.7987 (mp0) REVERT: B 97 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7145 (tpt-90) REVERT: B 166 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8454 (tp30) REVERT: C 11 LYS cc_start: 0.9492 (mmtm) cc_final: 0.9070 (mttp) REVERT: C 70 TRP cc_start: 0.8156 (OUTLIER) cc_final: 0.7357 (p-90) REVERT: C 71 CYS cc_start: 0.7730 (m) cc_final: 0.7468 (m) REVERT: C 97 ARG cc_start: 0.9197 (ttt180) cc_final: 0.8831 (ttt180) REVERT: C 122 TYR cc_start: 0.8853 (p90) cc_final: 0.8573 (p90) REVERT: C 129 ASN cc_start: 0.8500 (t0) cc_final: 0.7877 (t0) REVERT: C 130 MET cc_start: 0.8572 (tpt) cc_final: 0.8335 (tpp) REVERT: C 195 ASN cc_start: 0.9453 (m-40) cc_final: 0.9069 (p0) REVERT: C 209 TYR cc_start: 0.8869 (t80) cc_final: 0.8186 (t80) REVERT: C 257 LYS cc_start: 0.6447 (tptt) cc_final: 0.6225 (tmtt) REVERT: D 101 ASP cc_start: 0.8901 (t0) cc_final: 0.7930 (p0) REVERT: D 130 MET cc_start: 0.8839 (tpp) cc_final: 0.8596 (tpp) REVERT: D 132 ARG cc_start: 0.8958 (tmt170) cc_final: 0.8612 (tmm-80) REVERT: D 154 MET cc_start: 0.9226 (mtp) cc_final: 0.8610 (mtp) outliers start: 45 outliers final: 34 residues processed: 188 average time/residue: 0.1037 time to fit residues: 26.0032 Evaluate side-chains 188 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain B residue 31 TRP Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 70 TRP Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain D residue 71 CYS Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 206 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 12 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.087574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.060160 restraints weight = 19637.285| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 3.48 r_work: 0.2753 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 8648 Z= 0.243 Angle : 0.684 7.983 11783 Z= 0.343 Chirality : 0.047 0.136 1312 Planarity : 0.005 0.052 1459 Dihedral : 9.473 83.904 1221 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 5.79 % Allowed : 26.50 % Favored : 67.71 % 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: -0.10 (0.28), residues: 1000 helix: 0.45 (0.31), residues: 328 sheet: -1.08 (0.34), residues: 240 loop : 0.40 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 148 TYR 0.044 0.003 TYR A 79 PHE 0.015 0.001 PHE C 112 TRP 0.011 0.001 TRP C 70 HIS 0.003 0.001 HIS A 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.24 ( 8648) covalent geometry : angle 0.68355 / 0.34 (11783) hydrogen bonds : bond 0.03832 / 2.45 ( 261) hydrogen bonds : angle 4.86475 / 3.43 ( 699) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 148 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.9002 (tp) REVERT: A 79 TYR cc_start: 0.9435 (t80) cc_final: 0.8872 (t80) REVERT: A 101 ASP cc_start: 0.9099 (t0) cc_final: 0.8770 (t0) REVERT: A 166 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8374 (tp30) REVERT: A 185 LYS cc_start: 0.9219 (ptpp) cc_final: 0.8769 (ptmt) REVERT: B 97 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7164 (tpt-90) REVERT: B 130 MET cc_start: 0.8883 (tpt) cc_final: 0.8637 (tpt) REVERT: C 11 LYS cc_start: 0.9516 (mmtm) cc_final: 0.9110 (mttp) REVERT: C 65 TYR cc_start: 0.8618 (t80) cc_final: 0.8405 (t80) REVERT: C 70 TRP cc_start: 0.8164 (OUTLIER) cc_final: 0.7182 (p-90) REVERT: C 71 CYS cc_start: 0.7835 (m) cc_final: 0.7115 (m) REVERT: C 119 ARG cc_start: 0.9207 (ptp90) cc_final: 0.8979 (ptp90) REVERT: C 122 TYR cc_start: 0.8914 (p90) cc_final: 0.8547 (p90) REVERT: C 129 ASN cc_start: 0.8522 (t0) cc_final: 0.7954 (t0) REVERT: C 161 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8380 (tp30) REVERT: C 195 ASN cc_start: 0.9458 (m-40) cc_final: 0.9093 (p0) REVERT: C 209 TYR cc_start: 0.8905 (t80) cc_final: 0.8309 (t80) REVERT: D 101 ASP cc_start: 0.8933 (t0) cc_final: 0.7967 (p0) REVERT: D 132 ARG cc_start: 0.8974 (tmt170) cc_final: 0.8639 (tmm-80) REVERT: D 154 MET cc_start: 0.9247 (mtp) cc_final: 0.8648 (mtp) outliers start: 52 outliers final: 37 residues processed: 188 average time/residue: 0.1030 time to fit residues: 25.7890 Evaluate side-chains 173 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain B residue 31 TRP Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 70 TRP Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 71 CYS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 206 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 36 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.088897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.062111 restraints weight = 19181.793| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 3.49 r_work: 0.2788 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8648 Z= 0.155 Angle : 0.663 8.587 11783 Z= 0.332 Chirality : 0.046 0.142 1312 Planarity : 0.005 0.047 1459 Dihedral : 9.469 86.042 1221 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.79 % Allowed : 28.06 % Favored : 67.15 % 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: 0.02 (0.28), residues: 1000 helix: 0.56 (0.31), residues: 328 sheet: -0.99 (0.35), residues: 236 loop : 0.43 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 148 TYR 0.034 0.002 TYR A 79 PHE 0.012 0.001 PHE C 112 TRP 0.015 0.001 TRP C 72 HIS 0.004 0.001 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 8648) covalent geometry : angle 0.66284 / 0.33 (11783) hydrogen bonds : bond 0.03675 / 2.35 ( 261) hydrogen bonds : angle 4.82710 / 3.39 ( 699) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 149 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.9224 (mmtt) cc_final: 0.8926 (mptt) REVERT: A 79 TYR cc_start: 0.9415 (t80) cc_final: 0.9022 (t80) REVERT: A 101 ASP cc_start: 0.9110 (t0) cc_final: 0.8800 (t0) REVERT: A 166 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8297 (tp30) REVERT: A 185 LYS cc_start: 0.9200 (ptpp) cc_final: 0.8778 (ptmt) REVERT: A 239 GLU cc_start: 0.8589 (mt-10) cc_final: 0.7981 (mp0) REVERT: B 97 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7145 (tpt-90) REVERT: C 11 LYS cc_start: 0.9526 (mmtm) cc_final: 0.9150 (mttp) REVERT: C 65 TYR cc_start: 0.8603 (t80) cc_final: 0.8363 (t80) REVERT: C 70 TRP cc_start: 0.8171 (OUTLIER) cc_final: 0.7151 (p-90) REVERT: C 71 CYS cc_start: 0.7789 (m) cc_final: 0.7069 (m) REVERT: C 129 ASN cc_start: 0.8533 (t0) cc_final: 0.7976 (t0) REVERT: C 130 MET cc_start: 0.8596 (tpt) cc_final: 0.8281 (tpp) REVERT: C 195 ASN cc_start: 0.9456 (m-40) cc_final: 0.9085 (p0) REVERT: C 209 TYR cc_start: 0.8851 (t80) cc_final: 0.8301 (t80) REVERT: D 101 ASP cc_start: 0.8933 (t0) cc_final: 0.7950 (p0) REVERT: D 132 ARG cc_start: 0.8966 (tmt170) cc_final: 0.8627 (tmm-80) REVERT: D 154 MET cc_start: 0.9277 (mtp) cc_final: 0.8659 (mtp) outliers start: 43 outliers final: 35 residues processed: 180 average time/residue: 0.0853 time to fit residues: 20.8713 Evaluate side-chains 182 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 144 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain B residue 31 TRP Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 70 TRP Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 206 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 4 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.087607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.061025 restraints weight = 19313.457| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 3.40 r_work: 0.2773 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8648 Z= 0.194 Angle : 0.670 9.408 11783 Z= 0.336 Chirality : 0.046 0.145 1312 Planarity : 0.005 0.096 1459 Dihedral : 9.446 88.721 1221 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.68 % Allowed : 28.06 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.28), residues: 1000 helix: 0.58 (0.31), residues: 328 sheet: -1.03 (0.34), residues: 236 loop : 0.42 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 97 TYR 0.031 0.003 TYR A 79 PHE 0.012 0.001 PHE D 60 TRP 0.017 0.001 TRP C 72 HIS 0.003 0.001 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.19 ( 8648) covalent geometry : angle 0.67012 / 0.34 (11783) hydrogen bonds : bond 0.03615 / 2.32 ( 261) hydrogen bonds : angle 4.82051 / 3.39 ( 699) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 141 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.9198 (mmtt) cc_final: 0.8872 (mptt) REVERT: A 166 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8327 (tp30) REVERT: A 185 LYS cc_start: 0.9203 (ptpp) cc_final: 0.8803 (ptmt) REVERT: A 239 GLU cc_start: 0.8548 (mt-10) cc_final: 0.7971 (mp0) REVERT: B 97 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7150 (tpt-90) REVERT: C 11 LYS cc_start: 0.9528 (mmtm) cc_final: 0.9176 (mttp) REVERT: C 65 TYR cc_start: 0.8617 (t80) cc_final: 0.8383 (t80) REVERT: C 70 TRP cc_start: 0.8144 (OUTLIER) cc_final: 0.7059 (p-90) REVERT: C 71 CYS cc_start: 0.7807 (m) cc_final: 0.7099 (m) REVERT: C 122 TYR cc_start: 0.8943 (p90) cc_final: 0.8611 (p90) REVERT: C 129 ASN cc_start: 0.8556 (t0) cc_final: 0.7967 (t0) REVERT: C 161 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8376 (tp30) REVERT: C 195 ASN cc_start: 0.9440 (m-40) cc_final: 0.9099 (p0) REVERT: C 209 TYR cc_start: 0.8842 (t80) cc_final: 0.8279 (t80) REVERT: D 14 LYS cc_start: 0.9468 (tptp) cc_final: 0.9260 (tptm) REVERT: D 101 ASP cc_start: 0.8976 (t0) cc_final: 0.8462 (t0) REVERT: D 130 MET cc_start: 0.8961 (tpt) cc_final: 0.8636 (tpt) REVERT: D 132 ARG cc_start: 0.8968 (tmt170) cc_final: 0.8629 (tmm-80) REVERT: D 154 MET cc_start: 0.9237 (mtp) cc_final: 0.8693 (mtp) outliers start: 42 outliers final: 36 residues processed: 173 average time/residue: 0.0893 time to fit residues: 20.4604 Evaluate side-chains 182 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain B residue 31 TRP Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 70 TRP Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 206 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 48 optimal weight: 0.0050 chunk 80 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.090087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.063990 restraints weight = 19040.867| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 3.48 r_work: 0.2827 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8648 Z= 0.125 Angle : 0.664 9.158 11783 Z= 0.333 Chirality : 0.046 0.153 1312 Planarity : 0.005 0.068 1459 Dihedral : 9.402 88.117 1221 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.56 % Allowed : 29.40 % Favored : 67.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.13 (0.29), residues: 1000 helix: 0.65 (0.31), residues: 328 sheet: -0.99 (0.35), residues: 228 loop : 0.50 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 97 TYR 0.032 0.002 TYR A 79 PHE 0.015 0.001 PHE A 125 TRP 0.021 0.001 TRP C 72 HIS 0.007 0.001 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 8648) covalent geometry : angle 0.66405 / 0.33 (11783) hydrogen bonds : bond 0.03564 / 2.26 ( 261) hydrogen bonds : angle 4.76862 / 3.35 ( 699) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.9228 (mmtt) cc_final: 0.8925 (mptt) REVERT: A 101 ASP cc_start: 0.9107 (t0) cc_final: 0.8795 (t0) REVERT: A 166 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8234 (tp30) REVERT: A 185 LYS cc_start: 0.9184 (ptpp) cc_final: 0.8768 (ptmt) REVERT: A 239 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7846 (mp0) REVERT: C 11 LYS cc_start: 0.9520 (mmtm) cc_final: 0.9191 (mtmt) REVERT: C 65 TYR cc_start: 0.8572 (t80) cc_final: 0.8326 (t80) REVERT: C 70 TRP cc_start: 0.8152 (OUTLIER) cc_final: 0.7099 (p-90) REVERT: C 71 CYS cc_start: 0.7755 (m) cc_final: 0.7059 (m) REVERT: C 122 TYR cc_start: 0.8895 (p90) cc_final: 0.8544 (p90) REVERT: C 129 ASN cc_start: 0.8549 (t0) cc_final: 0.7975 (t0) REVERT: C 161 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8251 (tp30) REVERT: C 195 ASN cc_start: 0.9455 (m-40) cc_final: 0.9089 (p0) REVERT: C 209 TYR cc_start: 0.8756 (t80) cc_final: 0.7709 (t80) REVERT: D 14 LYS cc_start: 0.9446 (tptp) cc_final: 0.9216 (tptm) REVERT: D 101 ASP cc_start: 0.8942 (t0) cc_final: 0.8413 (t0) REVERT: D 132 ARG cc_start: 0.8956 (tmt170) cc_final: 0.8592 (tmm-80) REVERT: D 154 MET cc_start: 0.9288 (mtp) cc_final: 0.8727 (mtp) REVERT: D 166 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8482 (tp30) REVERT: D 209 TYR cc_start: 0.8930 (t80) cc_final: 0.7734 (t80) outliers start: 32 outliers final: 27 residues processed: 177 average time/residue: 0.0944 time to fit residues: 22.3945 Evaluate side-chains 177 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain B residue 31 TRP Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 70 TRP Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 166 GLU Chi-restraints excluded: chain D residue 206 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 33 optimal weight: 0.1980 chunk 95 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 16 optimal weight: 0.0870 chunk 45 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.090951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.063972 restraints weight = 19140.128| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.61 r_work: 0.2834 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8648 Z= 0.122 Angle : 0.657 9.082 11783 Z= 0.329 Chirality : 0.046 0.149 1312 Planarity : 0.005 0.082 1459 Dihedral : 9.341 85.620 1221 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.90 % Allowed : 29.18 % Favored : 66.93 % 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: 0.13 (0.29), residues: 1000 helix: 0.58 (0.31), residues: 328 sheet: -0.98 (0.35), residues: 228 loop : 0.56 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 97 TYR 0.024 0.002 TYR C 56 PHE 0.015 0.001 PHE A 125 TRP 0.023 0.001 TRP C 72 HIS 0.003 0.000 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 8648) covalent geometry : angle 0.65748 / 0.33 (11783) hydrogen bonds : bond 0.03423 / 2.17 ( 261) hydrogen bonds : angle 4.79176 / 3.35 ( 699) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1896.46 seconds wall clock time: 33 minutes 22.93 seconds (2002.93 seconds total)