Starting phenix.real_space_refine on Wed Mar 4 14:47:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a3b_15110/03_2026/8a3b_15110.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a3b_15110/03_2026/8a3b_15110.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a3b_15110/03_2026/8a3b_15110.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a3b_15110/03_2026/8a3b_15110.map" model { file = "/net/cci-nas-00/data/ceres_data/8a3b_15110/03_2026/8a3b_15110.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a3b_15110/03_2026/8a3b_15110.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 9646 2.51 5 N 2219 2.21 5 O 2499 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14448 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2064 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain breaks: 2 Chain: "B" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2064 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain breaks: 2 Chain: "C" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2064 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain breaks: 2 Chain: "D" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2064 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain breaks: 2 Chain: "E" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2064 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain breaks: 2 Chain: "F" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2064 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain breaks: 2 Chain: "G" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2064 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain breaks: 2 Time building chain proxies: 3.51, per 1000 atoms: 0.24 Number of scatterers: 14448 At special positions: 0 Unit cell: (106.869, 105.778, 109.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2499 8.00 N 2219 7.00 C 9646 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: 1.17 Conformation dependent library (CDL) restraints added in 427.4 milliseconds 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3500 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 7 sheets defined 79.1% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 32 through 61 Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 73 through 87 Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 99 through 108 removed outlier: 4.059A pdb=" N LEU A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 108 " --> pdb=" O TRP A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 130 Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 146 Processing helix chain 'A' and resid 196 through 205 Processing helix chain 'A' and resid 207 through 236 Processing helix chain 'A' and resid 237 through 240 Processing helix chain 'A' and resid 249 through 253 removed outlier: 3.971A pdb=" N LEU A 252 " --> pdb=" O SER A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 295 Proline residue: A 288 - end of helix removed outlier: 3.616A pdb=" N PHE A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 338 removed outlier: 3.507A pdb=" N LEU A 329 " --> pdb=" O ASN A 325 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 332 " --> pdb=" O SER A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 349 Processing helix chain 'B' and resid 32 through 61 Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 73 through 87 Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 99 through 108 removed outlier: 4.030A pdb=" N LEU B 103 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE B 108 " --> pdb=" O TRP B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 131 Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 146 Processing helix chain 'B' and resid 196 through 204 Processing helix chain 'B' and resid 206 through 236 Processing helix chain 'B' and resid 237 through 240 Processing helix chain 'B' and resid 249 through 255 removed outlier: 3.926A pdb=" N LEU B 252 " --> pdb=" O SER B 249 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN B 254 " --> pdb=" O VAL B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 295 Proline residue: B 288 - end of helix removed outlier: 3.609A pdb=" N PHE B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE B 295 " --> pdb=" O VAL B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 300 Processing helix chain 'B' and resid 325 through 338 removed outlier: 3.698A pdb=" N LEU B 329 " --> pdb=" O ASN B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 349 removed outlier: 3.528A pdb=" N LYS B 345 " --> pdb=" O LEU B 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 61 Proline residue: C 46 - end of helix Processing helix chain 'C' and resid 73 through 88 Processing helix chain 'C' and resid 99 through 108 removed outlier: 4.104A pdb=" N LEU C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS C 107 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE C 108 " --> pdb=" O TRP C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 131 Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 146 Processing helix chain 'C' and resid 196 through 205 removed outlier: 3.546A pdb=" N ASN C 204 " --> pdb=" O LYS C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 236 removed outlier: 3.534A pdb=" N LYS C 211 " --> pdb=" O HIS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 240 Processing helix chain 'C' and resid 249 through 255 removed outlier: 3.530A pdb=" N LEU C 252 " --> pdb=" O SER C 249 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN C 254 " --> pdb=" O VAL C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 295 removed outlier: 3.552A pdb=" N LEU C 274 " --> pdb=" O GLY C 270 " (cutoff:3.500A) Proline residue: C 288 - end of helix removed outlier: 3.573A pdb=" N PHE C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE C 295 " --> pdb=" O VAL C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 338 removed outlier: 3.660A pdb=" N LEU C 329 " --> pdb=" O ASN C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 349 removed outlier: 3.602A pdb=" N LYS C 345 " --> pdb=" O LEU C 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 61 Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 73 through 87 Processing helix chain 'D' and resid 88 through 90 No H-bonds generated for 'chain 'D' and resid 88 through 90' Processing helix chain 'D' and resid 99 through 108 removed outlier: 4.111A pdb=" N LEU D 103 " --> pdb=" O GLY D 99 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE D 108 " --> pdb=" O TRP D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 131 Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 147 Processing helix chain 'D' and resid 196 through 204 Processing helix chain 'D' and resid 206 through 236 removed outlier: 3.745A pdb=" N LYS D 211 " --> pdb=" O HIS D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 240 Processing helix chain 'D' and resid 249 through 255 removed outlier: 4.029A pdb=" N LEU D 252 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN D 254 " --> pdb=" O VAL D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 295 removed outlier: 3.666A pdb=" N LEU D 274 " --> pdb=" O GLY D 270 " (cutoff:3.500A) Proline residue: D 288 - end of helix removed outlier: 3.647A pdb=" N PHE D 294 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE D 295 " --> pdb=" O VAL D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 300 removed outlier: 3.829A pdb=" N GLN D 300 " --> pdb=" O ILE D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 338 removed outlier: 3.896A pdb=" N LEU D 329 " --> pdb=" O ASN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 349 Processing helix chain 'E' and resid 32 through 61 Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 73 through 87 Processing helix chain 'E' and resid 99 through 131 removed outlier: 4.082A pdb=" N LEU E 103 " --> pdb=" O GLY E 99 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS E 107 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE E 108 " --> pdb=" O TRP E 104 " (cutoff:3.500A) Proline residue: E 110 - end of helix Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 146 Processing helix chain 'E' and resid 196 through 204 Processing helix chain 'E' and resid 207 through 236 Processing helix chain 'E' and resid 237 through 240 Processing helix chain 'E' and resid 249 through 255 removed outlier: 3.924A pdb=" N LEU E 252 " --> pdb=" O SER E 249 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN E 254 " --> pdb=" O VAL E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 295 removed outlier: 3.654A pdb=" N LEU E 274 " --> pdb=" O GLY E 270 " (cutoff:3.500A) Proline residue: E 288 - end of helix removed outlier: 3.571A pdb=" N PHE E 294 " --> pdb=" O VAL E 290 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE E 295 " --> pdb=" O VAL E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 300 Processing helix chain 'E' and resid 325 through 338 removed outlier: 3.727A pdb=" N LEU E 329 " --> pdb=" O ASN E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 349 removed outlier: 3.543A pdb=" N LYS E 345 " --> pdb=" O LEU E 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 61 Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 73 through 87 Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'F' and resid 99 through 108 removed outlier: 4.310A pdb=" N LEU F 103 " --> pdb=" O GLY F 99 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE F 108 " --> pdb=" O TRP F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 146 Proline residue: F 123 - end of helix removed outlier: 4.234A pdb=" N ALA F 132 " --> pdb=" O ARG F 128 " (cutoff:3.500A) Proline residue: F 133 - end of helix Processing helix chain 'F' and resid 196 through 205 Processing helix chain 'F' and resid 206 through 236 removed outlier: 3.567A pdb=" N MET F 210 " --> pdb=" O SER F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 240 Processing helix chain 'F' and resid 249 through 255 removed outlier: 3.843A pdb=" N LEU F 252 " --> pdb=" O SER F 249 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASN F 254 " --> pdb=" O VAL F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 295 removed outlier: 3.635A pdb=" N LEU F 274 " --> pdb=" O GLY F 270 " (cutoff:3.500A) Proline residue: F 288 - end of helix removed outlier: 3.633A pdb=" N PHE F 294 " --> pdb=" O VAL F 290 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE F 295 " --> pdb=" O VAL F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 300 Processing helix chain 'F' and resid 325 through 338 removed outlier: 3.539A pdb=" N LEU F 329 " --> pdb=" O ASN F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 349 Processing helix chain 'G' and resid 32 through 61 Proline residue: G 46 - end of helix Processing helix chain 'G' and resid 73 through 87 Processing helix chain 'G' and resid 99 through 108 removed outlier: 3.980A pdb=" N LEU G 103 " --> pdb=" O GLY G 99 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS G 107 " --> pdb=" O LEU G 103 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE G 108 " --> pdb=" O TRP G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 131 Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 146 Processing helix chain 'G' and resid 196 through 205 Processing helix chain 'G' and resid 206 through 236 removed outlier: 3.612A pdb=" N MET G 210 " --> pdb=" O SER G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 240 Processing helix chain 'G' and resid 249 through 253 removed outlier: 3.965A pdb=" N LEU G 252 " --> pdb=" O SER G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 268 through 295 removed outlier: 3.539A pdb=" N LEU G 274 " --> pdb=" O GLY G 270 " (cutoff:3.500A) Proline residue: G 288 - end of helix removed outlier: 3.520A pdb=" N PHE G 294 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE G 295 " --> pdb=" O VAL G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 300 removed outlier: 3.767A pdb=" N GLN G 300 " --> pdb=" O PRO G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 338 removed outlier: 3.531A pdb=" N LEU G 329 " --> pdb=" O ASN G 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 341 through 349 removed outlier: 3.632A pdb=" N LYS G 345 " --> pdb=" O LEU G 341 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 67 removed outlier: 4.332A pdb=" N GLN A 263 " --> pdb=" O PHE A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 67 removed outlier: 4.320A pdb=" N GLN B 263 " --> pdb=" O PHE B 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 67 removed outlier: 4.343A pdb=" N GLN E 263 " --> pdb=" O PHE E 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 67 removed outlier: 4.476A pdb=" N GLN G 263 " --> pdb=" O PHE G 67 " (cutoff:3.500A) 991 hydrogen bonds defined for protein. 2892 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: 2.26 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4221 1.34 - 1.46: 3513 1.46 - 1.58: 6952 1.58 - 1.69: 0 1.69 - 1.81: 105 Bond restraints: 14791 Sorted by residual: bond pdb=" N HIS G 134 " pdb=" CA HIS G 134 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.28e-02 6.10e+03 5.55e+00 bond pdb=" N LEU C 28 " pdb=" CA LEU C 28 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.34e+00 bond pdb=" N LEU A 28 " pdb=" CA LEU A 28 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" N LEU B 28 " pdb=" CA LEU B 28 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N LEU G 28 " pdb=" CA LEU G 28 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 ... (remaining 14786 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 19460 1.33 - 2.66: 485 2.66 - 4.00: 66 4.00 - 5.33: 30 5.33 - 6.66: 7 Bond angle restraints: 20048 Sorted by residual: angle pdb=" C ILE E 287 " pdb=" CA ILE E 287 " pdb=" CB ILE E 287 " ideal model delta sigma weight residual 113.70 110.12 3.58 9.50e-01 1.11e+00 1.42e+01 angle pdb=" C PHE B 295 " pdb=" N ILE B 296 " pdb=" CA ILE B 296 " ideal model delta sigma weight residual 120.24 122.45 -2.21 6.30e-01 2.52e+00 1.23e+01 angle pdb=" C PHE D 295 " pdb=" N ILE D 296 " pdb=" CA ILE D 296 " ideal model delta sigma weight residual 120.24 122.36 -2.12 6.30e-01 2.52e+00 1.14e+01 angle pdb=" N LYS G 148 " pdb=" CA LYS G 148 " pdb=" C LYS G 148 " ideal model delta sigma weight residual 113.43 109.36 4.07 1.26e+00 6.30e-01 1.04e+01 angle pdb=" N ALA A 131 " pdb=" CA ALA A 131 " pdb=" CB ALA A 131 " ideal model delta sigma weight residual 114.17 110.52 3.65 1.14e+00 7.69e-01 1.03e+01 ... (remaining 20043 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.40: 7899 16.40 - 32.79: 671 32.79 - 49.19: 154 49.19 - 65.59: 51 65.59 - 81.99: 24 Dihedral angle restraints: 8799 sinusoidal: 3437 harmonic: 5362 Sorted by residual: dihedral pdb=" CA GLU C 145 " pdb=" C GLU C 145 " pdb=" N LEU C 146 " pdb=" CA LEU C 146 " ideal model delta harmonic sigma weight residual 180.00 161.28 18.72 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA GLU E 145 " pdb=" C GLU E 145 " pdb=" N LEU E 146 " pdb=" CA LEU E 146 " ideal model delta harmonic sigma weight residual 180.00 161.49 18.51 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA GLU F 145 " pdb=" C GLU F 145 " pdb=" N LEU F 146 " pdb=" CA LEU F 146 " ideal model delta harmonic sigma weight residual 180.00 161.87 18.13 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 8796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1693 0.029 - 0.058: 427 0.058 - 0.087: 185 0.087 - 0.117: 58 0.117 - 0.146: 10 Chirality restraints: 2373 Sorted by residual: chirality pdb=" CA ILE C 258 " pdb=" N ILE C 258 " pdb=" C ILE C 258 " pdb=" CB ILE C 258 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA LEU F 28 " pdb=" N LEU F 28 " pdb=" C LEU F 28 " pdb=" CB LEU F 28 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CA ILE A 258 " pdb=" N ILE A 258 " pdb=" C ILE A 258 " pdb=" CB ILE A 258 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 2370 not shown) Planarity restraints: 2394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 74 " 0.003 2.00e-02 2.50e+03 8.20e-03 1.68e+00 pdb=" CG TRP A 74 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP A 74 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 74 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 74 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 74 " -0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP A 74 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 74 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 74 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 74 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 128 " -0.104 9.50e-02 1.11e+02 4.70e-02 1.58e+00 pdb=" NE ARG A 128 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 128 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 128 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 128 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 333 " 0.009 2.00e-02 2.50e+03 9.07e-03 1.44e+00 pdb=" CG PHE B 333 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE B 333 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE B 333 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 333 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 333 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 333 " 0.001 2.00e-02 2.50e+03 ... (remaining 2391 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 120 2.65 - 3.21: 13993 3.21 - 3.78: 22510 3.78 - 4.34: 30452 4.34 - 4.90: 51494 Nonbonded interactions: 118569 Sorted by model distance: nonbonded pdb=" OD1 ASP G 147 " pdb=" OG SER G 343 " model vdw 2.091 3.040 nonbonded pdb=" OD1 ASP B 147 " pdb=" OG SER B 343 " model vdw 2.129 3.040 nonbonded pdb=" O TYR F 232 " pdb=" OG SER F 235 " model vdw 2.195 3.040 nonbonded pdb=" O TYR G 232 " pdb=" OG SER G 235 " model vdw 2.258 3.040 nonbonded pdb=" O TYR E 232 " pdb=" OG SER E 235 " model vdw 2.259 3.040 ... (remaining 118564 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.560 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 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 : 0.003 0.035 14791 Z= 0.136 Angle : 0.546 6.661 20048 Z= 0.333 Chirality : 0.034 0.146 2373 Planarity : 0.003 0.047 2394 Dihedral : 14.171 81.986 5299 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: 2.21 (0.20), residues: 1750 helix: 2.26 (0.14), residues: 1288 sheet: None (None), residues: 0 loop : -0.87 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 128 TYR 0.011 0.001 TYR B 111 PHE 0.020 0.001 PHE B 333 TRP 0.018 0.001 TRP B 74 HIS 0.004 0.001 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00262 (14791) covalent geometry : angle 0.54635 (20048) hydrogen bonds : bond 0.14254 ( 991) hydrogen bonds : angle 5.43924 ( 2892) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 449 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8616 (tp) cc_final: 0.8160 (tp) REVERT: A 50 ILE cc_start: 0.8141 (mt) cc_final: 0.7926 (tt) REVERT: A 51 SER cc_start: 0.7780 (m) cc_final: 0.7529 (p) REVERT: A 65 SER cc_start: 0.8337 (p) cc_final: 0.8082 (m) REVERT: A 83 TYR cc_start: 0.7661 (t80) cc_final: 0.7449 (t80) REVERT: A 118 ILE cc_start: 0.8312 (mm) cc_final: 0.8095 (mm) REVERT: A 233 TYR cc_start: 0.8254 (t80) cc_final: 0.7817 (t80) REVERT: B 36 LYS cc_start: 0.8330 (tppt) cc_final: 0.7907 (tppt) REVERT: B 48 LEU cc_start: 0.8583 (tp) cc_final: 0.8216 (tp) REVERT: B 203 LYS cc_start: 0.7902 (ttpt) cc_final: 0.7525 (ttpt) REVERT: B 224 LEU cc_start: 0.8201 (tp) cc_final: 0.7893 (tp) REVERT: B 234 PHE cc_start: 0.8579 (t80) cc_final: 0.8289 (t80) REVERT: B 349 VAL cc_start: 0.6444 (t) cc_final: 0.6108 (m) REVERT: C 36 LYS cc_start: 0.8430 (tmtt) cc_final: 0.7844 (tmtt) REVERT: C 48 LEU cc_start: 0.8599 (tp) cc_final: 0.8226 (tp) REVERT: C 51 SER cc_start: 0.8097 (m) cc_final: 0.7852 (p) REVERT: C 198 TYR cc_start: 0.7461 (t80) cc_final: 0.7227 (t80) REVERT: C 221 VAL cc_start: 0.8457 (t) cc_final: 0.8121 (p) REVERT: C 234 PHE cc_start: 0.8524 (t80) cc_final: 0.8213 (t80) REVERT: D 36 LYS cc_start: 0.8370 (tmtt) cc_final: 0.7783 (tmtt) REVERT: D 37 MET cc_start: 0.6877 (tpt) cc_final: 0.6580 (tpt) REVERT: D 89 GLN cc_start: 0.7760 (mt0) cc_final: 0.7126 (mt0) REVERT: D 104 TRP cc_start: 0.6781 (t-100) cc_final: 0.6504 (t-100) REVERT: D 203 LYS cc_start: 0.8235 (tmmt) cc_final: 0.7732 (tmmt) REVERT: D 221 VAL cc_start: 0.8207 (t) cc_final: 0.7975 (t) REVERT: E 51 SER cc_start: 0.7832 (m) cc_final: 0.7621 (p) REVERT: E 108 PHE cc_start: 0.8324 (m-80) cc_final: 0.7947 (m-80) REVERT: E 148 LYS cc_start: 0.6983 (mtpt) cc_final: 0.6747 (mtmt) REVERT: E 203 LYS cc_start: 0.8023 (tmmt) cc_final: 0.7809 (tmmt) REVERT: E 232 TYR cc_start: 0.7707 (t80) cc_final: 0.7357 (t80) REVERT: F 36 LYS cc_start: 0.8411 (tmtt) cc_final: 0.8076 (tmtt) REVERT: G 47 LEU cc_start: 0.8431 (mt) cc_final: 0.8159 (mp) REVERT: G 48 LEU cc_start: 0.8575 (tp) cc_final: 0.8055 (tp) REVERT: G 50 ILE cc_start: 0.8137 (mt) cc_final: 0.7876 (tt) REVERT: G 202 LYS cc_start: 0.7365 (mmtt) cc_final: 0.7109 (mmtt) REVERT: G 203 LYS cc_start: 0.7711 (tttt) cc_final: 0.7490 (tttt) outliers start: 0 outliers final: 0 residues processed: 449 average time/residue: 0.1212 time to fit residues: 79.7332 Evaluate side-chains 377 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.0670 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 337 ASN C 337 ASN D 134 HIS E 89 GLN E 207 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.146293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.131422 restraints weight = 18933.759| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.85 r_work: 0.3565 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14791 Z= 0.180 Angle : 0.557 6.722 20048 Z= 0.283 Chirality : 0.040 0.229 2373 Planarity : 0.004 0.038 2394 Dihedral : 3.847 21.033 1904 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.64 % Allowed : 10.27 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.21 (0.20), residues: 1750 helix: 2.12 (0.14), residues: 1309 sheet: None (None), residues: 0 loop : -0.54 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 29 TYR 0.016 0.001 TYR C 121 PHE 0.017 0.001 PHE E 234 TRP 0.015 0.002 TRP D 74 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00427 (14791) covalent geometry : angle 0.55661 (20048) hydrogen bonds : bond 0.04217 ( 991) hydrogen bonds : angle 4.19306 ( 2892) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 394 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8548 (tp) cc_final: 0.8155 (tp) REVERT: A 50 ILE cc_start: 0.8230 (mt) cc_final: 0.7933 (tt) REVERT: A 51 SER cc_start: 0.8096 (m) cc_final: 0.7756 (p) REVERT: A 228 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8196 (mt) REVERT: A 231 SER cc_start: 0.8487 (t) cc_final: 0.8228 (p) REVERT: A 233 TYR cc_start: 0.8455 (t80) cc_final: 0.8093 (t80) REVERT: A 256 SER cc_start: 0.8494 (OUTLIER) cc_final: 0.8159 (m) REVERT: B 66 CYS cc_start: 0.7782 (t) cc_final: 0.7392 (m) REVERT: B 224 LEU cc_start: 0.8416 (tp) cc_final: 0.8179 (tp) REVERT: B 271 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8067 (tt) REVERT: B 349 VAL cc_start: 0.6924 (t) cc_final: 0.6530 (m) REVERT: C 36 LYS cc_start: 0.8677 (tmtt) cc_final: 0.8083 (tmtt) REVERT: C 51 SER cc_start: 0.8260 (m) cc_final: 0.8032 (p) REVERT: C 115 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8283 (tt) REVERT: C 234 PHE cc_start: 0.8697 (t80) cc_final: 0.8262 (t80) REVERT: C 249 SER cc_start: 0.8415 (t) cc_final: 0.7960 (p) REVERT: C 265 LYS cc_start: 0.8532 (tptp) cc_final: 0.8328 (tptt) REVERT: D 36 LYS cc_start: 0.8561 (tmtt) cc_final: 0.7993 (tmtt) REVERT: D 37 MET cc_start: 0.7975 (tpt) cc_final: 0.7598 (tpt) REVERT: D 203 LYS cc_start: 0.8418 (tmmt) cc_final: 0.7934 (tmmt) REVERT: D 229 TYR cc_start: 0.8317 (t80) cc_final: 0.8069 (t80) REVERT: D 265 LYS cc_start: 0.8606 (tptp) cc_final: 0.8401 (tptt) REVERT: E 36 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8447 (tmtt) REVERT: E 50 ILE cc_start: 0.8116 (mt) cc_final: 0.7801 (tt) REVERT: E 51 SER cc_start: 0.8162 (m) cc_final: 0.7816 (p) REVERT: E 203 LYS cc_start: 0.8254 (tmmt) cc_final: 0.8023 (tmmt) REVERT: E 221 VAL cc_start: 0.8620 (t) cc_final: 0.8396 (t) REVERT: E 228 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8166 (mt) REVERT: E 265 LYS cc_start: 0.8541 (mmmt) cc_final: 0.8329 (tptp) REVERT: E 293 THR cc_start: 0.8631 (m) cc_final: 0.8254 (m) REVERT: E 336 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7435 (tm-30) REVERT: F 36 LYS cc_start: 0.8581 (tmtt) cc_final: 0.8184 (tmtt) REVERT: F 115 LEU cc_start: 0.8508 (tp) cc_final: 0.8297 (tt) REVERT: G 65 SER cc_start: 0.8681 (p) cc_final: 0.8475 (m) REVERT: G 115 LEU cc_start: 0.8369 (tp) cc_final: 0.8161 (tt) outliers start: 27 outliers final: 11 residues processed: 406 average time/residue: 0.1220 time to fit residues: 72.5155 Evaluate side-chains 399 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 382 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 337 ASN Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 271 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 39 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 6 optimal weight: 0.0670 chunk 26 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN B 207 HIS C 89 GLN C 337 ASN D 134 HIS ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 ASN ** G 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.146554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.131623 restraints weight = 19160.625| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 1.89 r_work: 0.3569 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14791 Z= 0.134 Angle : 0.504 6.581 20048 Z= 0.255 Chirality : 0.038 0.240 2373 Planarity : 0.003 0.034 2394 Dihedral : 3.768 20.976 1904 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.19 % Allowed : 12.16 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.21 (0.20), residues: 1750 helix: 2.09 (0.14), residues: 1309 sheet: None (None), residues: 0 loop : -0.43 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 29 TYR 0.022 0.001 TYR C 121 PHE 0.017 0.001 PHE F 108 TRP 0.014 0.002 TRP F 104 HIS 0.007 0.001 HIS E 207 Details of bonding type rmsd covalent geometry : bond 0.00309 (14791) covalent geometry : angle 0.50354 (20048) hydrogen bonds : bond 0.03882 ( 991) hydrogen bonds : angle 3.98210 ( 2892) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 395 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8566 (tp) cc_final: 0.8208 (tp) REVERT: A 50 ILE cc_start: 0.8225 (mt) cc_final: 0.7933 (tt) REVERT: A 51 SER cc_start: 0.8052 (m) cc_final: 0.7750 (p) REVERT: A 115 LEU cc_start: 0.8486 (tp) cc_final: 0.8247 (tt) REVERT: A 228 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8144 (mt) REVERT: A 231 SER cc_start: 0.8487 (t) cc_final: 0.8234 (m) REVERT: A 233 TYR cc_start: 0.8492 (t80) cc_final: 0.8193 (t80) REVERT: B 36 LYS cc_start: 0.8722 (tppt) cc_final: 0.8262 (tppt) REVERT: B 224 LEU cc_start: 0.8414 (tp) cc_final: 0.8209 (tp) REVERT: B 271 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.8099 (tt) REVERT: B 349 VAL cc_start: 0.7053 (t) cc_final: 0.6739 (m) REVERT: C 48 LEU cc_start: 0.8633 (tp) cc_final: 0.8308 (tp) REVERT: C 115 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8295 (tt) REVERT: C 234 PHE cc_start: 0.8678 (t80) cc_final: 0.8253 (t80) REVERT: C 249 SER cc_start: 0.8381 (t) cc_final: 0.7891 (p) REVERT: D 36 LYS cc_start: 0.8543 (tmtt) cc_final: 0.8000 (tmtt) REVERT: D 37 MET cc_start: 0.7876 (tpt) cc_final: 0.7527 (tpt) REVERT: D 203 LYS cc_start: 0.8411 (tmmt) cc_final: 0.7940 (tmmt) REVERT: D 265 LYS cc_start: 0.8637 (tptp) cc_final: 0.8386 (tptt) REVERT: E 36 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8395 (tmtt) REVERT: E 50 ILE cc_start: 0.8105 (mt) cc_final: 0.7801 (tt) REVERT: E 51 SER cc_start: 0.8137 (m) cc_final: 0.7831 (p) REVERT: E 108 PHE cc_start: 0.8392 (m-80) cc_final: 0.8085 (m-80) REVERT: E 203 LYS cc_start: 0.8171 (tmmt) cc_final: 0.7910 (tmmt) REVERT: E 293 THR cc_start: 0.8489 (m) cc_final: 0.8142 (m) REVERT: F 36 LYS cc_start: 0.8592 (tmtt) cc_final: 0.8237 (tmtt) REVERT: F 83 TYR cc_start: 0.8257 (t80) cc_final: 0.8025 (t80) REVERT: F 203 LYS cc_start: 0.8098 (tttt) cc_final: 0.7874 (tttt) REVERT: F 252 LEU cc_start: 0.8154 (mt) cc_final: 0.7824 (mt) REVERT: G 115 LEU cc_start: 0.8359 (tp) cc_final: 0.8135 (tt) REVERT: G 122 LEU cc_start: 0.8284 (mt) cc_final: 0.8007 (mp) REVERT: G 249 SER cc_start: 0.8250 (m) cc_final: 0.8016 (p) outliers start: 36 outliers final: 15 residues processed: 407 average time/residue: 0.1156 time to fit residues: 68.8985 Evaluate side-chains 404 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 385 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 337 ASN Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 271 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 18 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 152 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 146 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 337 ASN ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 GLN F 337 ASN ** G 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.150825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.136211 restraints weight = 19017.462| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 1.90 r_work: 0.3568 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14791 Z= 0.144 Angle : 0.513 7.150 20048 Z= 0.258 Chirality : 0.038 0.204 2373 Planarity : 0.003 0.032 2394 Dihedral : 3.758 21.173 1904 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.37 % Allowed : 14.04 % Favored : 83.59 % 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: 2.20 (0.20), residues: 1750 helix: 2.06 (0.14), residues: 1309 sheet: None (None), residues: 0 loop : -0.35 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 29 TYR 0.024 0.001 TYR B 121 PHE 0.016 0.001 PHE G 243 TRP 0.014 0.002 TRP F 104 HIS 0.005 0.001 HIS E 207 Details of bonding type rmsd covalent geometry : bond 0.00335 (14791) covalent geometry : angle 0.51256 (20048) hydrogen bonds : bond 0.03779 ( 991) hydrogen bonds : angle 3.91665 ( 2892) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 383 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8526 (tp) cc_final: 0.8172 (tp) REVERT: A 50 ILE cc_start: 0.8226 (mt) cc_final: 0.7920 (tt) REVERT: A 51 SER cc_start: 0.8048 (m) cc_final: 0.7713 (p) REVERT: A 228 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8115 (mt) REVERT: A 231 SER cc_start: 0.8450 (t) cc_final: 0.8200 (m) REVERT: A 233 TYR cc_start: 0.8473 (t80) cc_final: 0.8175 (t80) REVERT: A 256 SER cc_start: 0.8504 (OUTLIER) cc_final: 0.8184 (m) REVERT: A 274 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7717 (mp) REVERT: B 36 LYS cc_start: 0.8739 (tppt) cc_final: 0.8261 (tppt) REVERT: B 224 LEU cc_start: 0.8405 (tp) cc_final: 0.8203 (tp) REVERT: B 228 ILE cc_start: 0.8501 (tp) cc_final: 0.8236 (tp) REVERT: B 271 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8071 (tt) REVERT: B 349 VAL cc_start: 0.6828 (t) cc_final: 0.6559 (m) REVERT: C 52 LEU cc_start: 0.8436 (mm) cc_final: 0.8234 (mp) REVERT: C 115 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8214 (tt) REVERT: C 234 PHE cc_start: 0.8697 (t80) cc_final: 0.8274 (t80) REVERT: D 36 LYS cc_start: 0.8562 (tmtt) cc_final: 0.7995 (tmtt) REVERT: D 37 MET cc_start: 0.7948 (tpt) cc_final: 0.7586 (tpt) REVERT: D 203 LYS cc_start: 0.8232 (tmmt) cc_final: 0.7763 (tmmt) REVERT: E 36 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8400 (tmtt) REVERT: E 50 ILE cc_start: 0.8134 (mt) cc_final: 0.7815 (tt) REVERT: E 51 SER cc_start: 0.8141 (m) cc_final: 0.7831 (p) REVERT: E 108 PHE cc_start: 0.8403 (m-80) cc_final: 0.8036 (m-80) REVERT: E 203 LYS cc_start: 0.8135 (tmmt) cc_final: 0.7863 (tmmt) REVERT: E 293 THR cc_start: 0.8447 (m) cc_final: 0.8115 (m) REVERT: F 36 LYS cc_start: 0.8569 (tmtt) cc_final: 0.8249 (tmtt) REVERT: F 83 TYR cc_start: 0.8244 (t80) cc_final: 0.8029 (t80) REVERT: G 50 ILE cc_start: 0.8233 (mt) cc_final: 0.7970 (tt) REVERT: G 115 LEU cc_start: 0.8308 (tp) cc_final: 0.8067 (tt) REVERT: G 122 LEU cc_start: 0.8242 (mt) cc_final: 0.7958 (mp) REVERT: G 211 LYS cc_start: 0.8140 (mtpt) cc_final: 0.7940 (ttpt) REVERT: G 249 SER cc_start: 0.8240 (m) cc_final: 0.7977 (p) outliers start: 39 outliers final: 20 residues processed: 399 average time/residue: 0.1199 time to fit residues: 70.1360 Evaluate side-chains 410 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 384 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 274 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 163 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 94 optimal weight: 1.9990 chunk 49 optimal weight: 0.0980 chunk 168 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 104 optimal weight: 0.0770 chunk 84 optimal weight: 0.6980 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN B 207 HIS C 337 ASN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN G 90 GLN ** G 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.152279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.137650 restraints weight = 18900.409| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.91 r_work: 0.3585 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14791 Z= 0.107 Angle : 0.488 6.604 20048 Z= 0.244 Chirality : 0.037 0.201 2373 Planarity : 0.003 0.038 2394 Dihedral : 3.648 20.396 1904 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.43 % Allowed : 15.14 % Favored : 82.43 % 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: 2.32 (0.20), residues: 1750 helix: 2.18 (0.14), residues: 1302 sheet: None (None), residues: 0 loop : -0.37 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 29 TYR 0.021 0.001 TYR B 121 PHE 0.016 0.001 PHE G 67 TRP 0.018 0.001 TRP F 104 HIS 0.004 0.001 HIS F 207 Details of bonding type rmsd covalent geometry : bond 0.00234 (14791) covalent geometry : angle 0.48772 (20048) hydrogen bonds : bond 0.03437 ( 991) hydrogen bonds : angle 3.80872 ( 2892) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 389 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8450 (tp) cc_final: 0.8055 (tp) REVERT: A 50 ILE cc_start: 0.8193 (mt) cc_final: 0.7890 (tt) REVERT: A 51 SER cc_start: 0.7973 (m) cc_final: 0.7698 (p) REVERT: A 228 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8134 (mt) REVERT: A 231 SER cc_start: 0.8453 (t) cc_final: 0.8213 (m) REVERT: A 232 TYR cc_start: 0.8357 (t80) cc_final: 0.8122 (t80) REVERT: A 233 TYR cc_start: 0.8467 (t80) cc_final: 0.8221 (t80) REVERT: A 256 SER cc_start: 0.8490 (OUTLIER) cc_final: 0.8153 (m) REVERT: A 274 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7628 (mp) REVERT: B 36 LYS cc_start: 0.8802 (tppt) cc_final: 0.8315 (tppt) REVERT: B 198 TYR cc_start: 0.8144 (t80) cc_final: 0.7811 (t80) REVERT: B 224 LEU cc_start: 0.8384 (tp) cc_final: 0.8183 (tp) REVERT: B 228 ILE cc_start: 0.8458 (tp) cc_final: 0.8175 (tp) REVERT: B 271 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.8032 (tt) REVERT: B 349 VAL cc_start: 0.6990 (t) cc_final: 0.6698 (m) REVERT: C 52 LEU cc_start: 0.8421 (mm) cc_final: 0.8209 (mp) REVERT: C 106 HIS cc_start: 0.8234 (m-70) cc_final: 0.7896 (m90) REVERT: C 115 LEU cc_start: 0.8422 (tp) cc_final: 0.8186 (tt) REVERT: C 198 TYR cc_start: 0.7842 (t80) cc_final: 0.7557 (t80) REVERT: C 234 PHE cc_start: 0.8649 (t80) cc_final: 0.8239 (t80) REVERT: D 36 LYS cc_start: 0.8542 (tmtt) cc_final: 0.7957 (tmtt) REVERT: D 37 MET cc_start: 0.7924 (tpt) cc_final: 0.7520 (tpt) REVERT: D 52 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8245 (mp) REVERT: D 203 LYS cc_start: 0.8268 (tmmt) cc_final: 0.7858 (tmmt) REVERT: D 265 LYS cc_start: 0.8553 (tptp) cc_final: 0.8345 (tptt) REVERT: E 36 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8355 (tmtt) REVERT: E 50 ILE cc_start: 0.8122 (mt) cc_final: 0.7816 (tt) REVERT: E 51 SER cc_start: 0.8131 (m) cc_final: 0.7826 (p) REVERT: E 108 PHE cc_start: 0.8350 (m-80) cc_final: 0.8008 (m-80) REVERT: E 203 LYS cc_start: 0.8117 (tmmt) cc_final: 0.7827 (ttpp) REVERT: E 234 PHE cc_start: 0.8467 (t80) cc_final: 0.8257 (t80) REVERT: F 36 LYS cc_start: 0.8580 (tmtt) cc_final: 0.8279 (tmtt) REVERT: F 37 MET cc_start: 0.8222 (tpt) cc_final: 0.7791 (tpt) REVERT: F 83 TYR cc_start: 0.8233 (t80) cc_final: 0.8030 (t80) REVERT: G 115 LEU cc_start: 0.8268 (tp) cc_final: 0.8013 (tt) REVERT: G 122 LEU cc_start: 0.8239 (mt) cc_final: 0.7952 (mp) REVERT: G 249 SER cc_start: 0.8225 (m) cc_final: 0.7970 (p) outliers start: 40 outliers final: 20 residues processed: 407 average time/residue: 0.1181 time to fit residues: 70.5909 Evaluate side-chains 409 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 383 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 337 ASN Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 274 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 134 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 131 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 163 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS A 337 ASN C 337 ASN E 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.151203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.136690 restraints weight = 18933.864| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.89 r_work: 0.3579 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14791 Z= 0.145 Angle : 0.505 7.594 20048 Z= 0.253 Chirality : 0.038 0.201 2373 Planarity : 0.003 0.039 2394 Dihedral : 3.667 20.514 1904 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.31 % Allowed : 16.35 % Favored : 81.34 % 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: 2.30 (0.20), residues: 1750 helix: 2.16 (0.14), residues: 1302 sheet: None (None), residues: 0 loop : -0.36 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 29 TYR 0.022 0.001 TYR B 121 PHE 0.014 0.001 PHE G 243 TRP 0.019 0.002 TRP F 104 HIS 0.008 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00341 (14791) covalent geometry : angle 0.50454 (20048) hydrogen bonds : bond 0.03665 ( 991) hydrogen bonds : angle 3.83088 ( 2892) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 387 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8452 (tp) cc_final: 0.8059 (tp) REVERT: A 50 ILE cc_start: 0.8216 (mt) cc_final: 0.7918 (tt) REVERT: A 51 SER cc_start: 0.8035 (m) cc_final: 0.7744 (p) REVERT: A 228 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8131 (mt) REVERT: A 231 SER cc_start: 0.8458 (t) cc_final: 0.8228 (m) REVERT: A 232 TYR cc_start: 0.8375 (t80) cc_final: 0.8174 (t80) REVERT: A 256 SER cc_start: 0.8526 (OUTLIER) cc_final: 0.8197 (m) REVERT: A 274 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7689 (mp) REVERT: B 135 LEU cc_start: 0.7771 (tp) cc_final: 0.7230 (tp) REVERT: B 198 TYR cc_start: 0.8161 (t80) cc_final: 0.7960 (t80) REVERT: B 228 ILE cc_start: 0.8472 (tp) cc_final: 0.8188 (tp) REVERT: B 271 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.8068 (tt) REVERT: B 349 VAL cc_start: 0.7009 (t) cc_final: 0.6775 (m) REVERT: C 52 LEU cc_start: 0.8454 (mm) cc_final: 0.8243 (mp) REVERT: C 115 LEU cc_start: 0.8404 (tp) cc_final: 0.8182 (tt) REVERT: C 198 TYR cc_start: 0.7886 (t80) cc_final: 0.7607 (t80) REVERT: C 234 PHE cc_start: 0.8675 (t80) cc_final: 0.8287 (t80) REVERT: D 36 LYS cc_start: 0.8565 (tmtt) cc_final: 0.7981 (tmtt) REVERT: D 37 MET cc_start: 0.7901 (tpt) cc_final: 0.7545 (tpt) REVERT: D 52 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8213 (mp) REVERT: D 203 LYS cc_start: 0.8230 (tmmt) cc_final: 0.7836 (tmmt) REVERT: E 36 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8409 (tmtt) REVERT: E 51 SER cc_start: 0.8162 (m) cc_final: 0.7844 (p) REVERT: E 108 PHE cc_start: 0.8404 (m-80) cc_final: 0.8036 (m-80) REVERT: E 203 LYS cc_start: 0.8127 (tmmt) cc_final: 0.7843 (ttpp) REVERT: E 234 PHE cc_start: 0.8508 (t80) cc_final: 0.8307 (t80) REVERT: F 36 LYS cc_start: 0.8591 (tmtt) cc_final: 0.8290 (tmtt) REVERT: F 37 MET cc_start: 0.8296 (tpt) cc_final: 0.7890 (tpt) REVERT: F 83 TYR cc_start: 0.8233 (t80) cc_final: 0.7986 (t80) REVERT: F 271 ILE cc_start: 0.8600 (mm) cc_final: 0.8116 (tp) REVERT: G 115 LEU cc_start: 0.8284 (tp) cc_final: 0.8042 (tt) REVERT: G 122 LEU cc_start: 0.8264 (mt) cc_final: 0.7968 (mp) REVERT: G 211 LYS cc_start: 0.8147 (ttpt) cc_final: 0.7943 (ttmt) REVERT: G 249 SER cc_start: 0.8225 (m) cc_final: 0.7978 (p) outliers start: 38 outliers final: 22 residues processed: 405 average time/residue: 0.1153 time to fit residues: 68.3927 Evaluate side-chains 410 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 382 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 271 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 68 optimal weight: 2.9990 chunk 104 optimal weight: 0.0030 chunk 102 optimal weight: 0.8980 chunk 150 optimal weight: 0.0040 chunk 48 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 171 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 overall best weight: 0.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS A 337 ASN B 207 HIS D 63 GLN D 100 ASN F 337 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.152559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.137987 restraints weight = 18783.177| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.91 r_work: 0.3588 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14791 Z= 0.111 Angle : 0.489 7.923 20048 Z= 0.243 Chirality : 0.036 0.197 2373 Planarity : 0.003 0.039 2394 Dihedral : 3.586 20.047 1904 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.37 % Allowed : 16.47 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.36 (0.20), residues: 1750 helix: 2.21 (0.14), residues: 1302 sheet: None (None), residues: 0 loop : -0.37 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 29 TYR 0.019 0.001 TYR B 121 PHE 0.013 0.001 PHE A 54 TRP 0.021 0.001 TRP F 104 HIS 0.005 0.001 HIS F 207 Details of bonding type rmsd covalent geometry : bond 0.00250 (14791) covalent geometry : angle 0.48869 (20048) hydrogen bonds : bond 0.03406 ( 991) hydrogen bonds : angle 3.75706 ( 2892) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 388 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8430 (tp) cc_final: 0.8049 (tp) REVERT: A 50 ILE cc_start: 0.8221 (mt) cc_final: 0.7922 (tt) REVERT: A 51 SER cc_start: 0.8015 (m) cc_final: 0.7731 (p) REVERT: A 228 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8075 (mt) REVERT: A 231 SER cc_start: 0.8439 (t) cc_final: 0.8208 (m) REVERT: A 233 TYR cc_start: 0.8363 (t80) cc_final: 0.8142 (t80) REVERT: A 256 SER cc_start: 0.8520 (OUTLIER) cc_final: 0.8187 (m) REVERT: A 274 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7629 (mp) REVERT: B 198 TYR cc_start: 0.8145 (t80) cc_final: 0.7935 (t80) REVERT: B 228 ILE cc_start: 0.8418 (tp) cc_final: 0.8113 (tp) REVERT: B 271 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.8030 (tt) REVERT: B 349 VAL cc_start: 0.7047 (t) cc_final: 0.6800 (m) REVERT: C 52 LEU cc_start: 0.8316 (mm) cc_final: 0.8091 (mp) REVERT: C 106 HIS cc_start: 0.8251 (m-70) cc_final: 0.7932 (m90) REVERT: C 115 LEU cc_start: 0.8366 (tp) cc_final: 0.8128 (tt) REVERT: C 198 TYR cc_start: 0.7839 (t80) cc_final: 0.7567 (t80) REVERT: C 234 PHE cc_start: 0.8643 (t80) cc_final: 0.8260 (t80) REVERT: D 36 LYS cc_start: 0.8590 (tmtt) cc_final: 0.7967 (tmtt) REVERT: D 37 MET cc_start: 0.7948 (tpt) cc_final: 0.7560 (tpt) REVERT: D 52 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8228 (mp) REVERT: D 203 LYS cc_start: 0.8248 (tmmt) cc_final: 0.7866 (tmmt) REVERT: D 265 LYS cc_start: 0.8572 (tptp) cc_final: 0.8366 (tptt) REVERT: E 36 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8385 (tmtt) REVERT: E 50 ILE cc_start: 0.8130 (mt) cc_final: 0.7821 (tt) REVERT: E 51 SER cc_start: 0.8117 (m) cc_final: 0.7772 (p) REVERT: E 56 GLN cc_start: 0.6682 (OUTLIER) cc_final: 0.6307 (mm-40) REVERT: E 108 PHE cc_start: 0.8246 (m-80) cc_final: 0.7896 (m-80) REVERT: E 203 LYS cc_start: 0.8126 (tmmt) cc_final: 0.7819 (ttpp) REVERT: E 253 LYS cc_start: 0.8682 (ttmm) cc_final: 0.8426 (ttmm) REVERT: F 36 LYS cc_start: 0.8588 (tmtt) cc_final: 0.8276 (tmtt) REVERT: F 37 MET cc_start: 0.8290 (tpt) cc_final: 0.7868 (tpt) REVERT: F 83 TYR cc_start: 0.8229 (t80) cc_final: 0.7992 (t80) REVERT: G 115 LEU cc_start: 0.8277 (tp) cc_final: 0.8013 (tt) REVERT: G 122 LEU cc_start: 0.8248 (mt) cc_final: 0.7954 (mp) REVERT: G 202 LYS cc_start: 0.7544 (mmtt) cc_final: 0.7309 (mmtt) REVERT: G 249 SER cc_start: 0.8213 (m) cc_final: 0.7977 (p) outliers start: 39 outliers final: 23 residues processed: 406 average time/residue: 0.1179 time to fit residues: 70.3240 Evaluate side-chains 414 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 384 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 337 ASN Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 271 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 15 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 172 optimal weight: 0.0470 chunk 100 optimal weight: 3.9990 chunk 10 optimal weight: 0.3980 chunk 56 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 156 optimal weight: 0.0070 chunk 89 optimal weight: 0.8980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS A 337 ASN C 100 ASN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.152786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.138172 restraints weight = 18803.757| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.91 r_work: 0.3598 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14791 Z= 0.109 Angle : 0.493 7.285 20048 Z= 0.245 Chirality : 0.036 0.183 2373 Planarity : 0.003 0.039 2394 Dihedral : 3.542 19.586 1904 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.01 % Allowed : 17.08 % Favored : 80.91 % 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: 2.43 (0.20), residues: 1750 helix: 2.27 (0.14), residues: 1302 sheet: None (None), residues: 0 loop : -0.37 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 75 TYR 0.019 0.001 TYR A 212 PHE 0.015 0.001 PHE F 108 TRP 0.022 0.001 TRP F 104 HIS 0.005 0.001 HIS F 207 Details of bonding type rmsd covalent geometry : bond 0.00241 (14791) covalent geometry : angle 0.49282 (20048) hydrogen bonds : bond 0.03347 ( 991) hydrogen bonds : angle 3.72669 ( 2892) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 390 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8406 (tp) cc_final: 0.8028 (tp) REVERT: A 50 ILE cc_start: 0.8201 (mt) cc_final: 0.7901 (tt) REVERT: A 51 SER cc_start: 0.7989 (m) cc_final: 0.7711 (p) REVERT: A 115 LEU cc_start: 0.8416 (tp) cc_final: 0.8197 (tt) REVERT: A 228 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8070 (mt) REVERT: A 231 SER cc_start: 0.8433 (t) cc_final: 0.8198 (m) REVERT: A 233 TYR cc_start: 0.8383 (t80) cc_final: 0.8150 (t80) REVERT: A 274 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7652 (mp) REVERT: B 135 LEU cc_start: 0.7326 (tp) cc_final: 0.6964 (mp) REVERT: B 228 ILE cc_start: 0.8422 (tp) cc_final: 0.8113 (tp) REVERT: B 271 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.8038 (tt) REVERT: B 349 VAL cc_start: 0.7045 (t) cc_final: 0.6784 (m) REVERT: C 52 LEU cc_start: 0.8311 (mm) cc_final: 0.8081 (mp) REVERT: C 106 HIS cc_start: 0.8242 (m-70) cc_final: 0.7921 (m90) REVERT: C 115 LEU cc_start: 0.8339 (tp) cc_final: 0.8114 (tt) REVERT: C 198 TYR cc_start: 0.7813 (t80) cc_final: 0.7539 (t80) REVERT: C 234 PHE cc_start: 0.8650 (t80) cc_final: 0.8254 (t80) REVERT: D 36 LYS cc_start: 0.8595 (tmtt) cc_final: 0.8004 (tmtt) REVERT: D 37 MET cc_start: 0.7960 (tpt) cc_final: 0.7573 (tpt) REVERT: D 52 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8247 (mp) REVERT: D 203 LYS cc_start: 0.8237 (tmmt) cc_final: 0.7869 (tmmt) REVERT: E 36 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8362 (tmtt) REVERT: E 50 ILE cc_start: 0.8125 (mt) cc_final: 0.7819 (tt) REVERT: E 51 SER cc_start: 0.8109 (m) cc_final: 0.7770 (p) REVERT: E 56 GLN cc_start: 0.6622 (OUTLIER) cc_final: 0.6330 (mm-40) REVERT: E 108 PHE cc_start: 0.8221 (m-80) cc_final: 0.7868 (m-80) REVERT: E 203 LYS cc_start: 0.8110 (tmmt) cc_final: 0.7789 (ttpp) REVERT: E 253 LYS cc_start: 0.8727 (ttmm) cc_final: 0.8492 (ttmm) REVERT: F 36 LYS cc_start: 0.8594 (tmtt) cc_final: 0.8253 (tmtt) REVERT: F 37 MET cc_start: 0.8286 (tpt) cc_final: 0.7866 (tpt) REVERT: F 83 TYR cc_start: 0.8226 (t80) cc_final: 0.7914 (t80) REVERT: F 249 SER cc_start: 0.8316 (m) cc_final: 0.7976 (p) REVERT: G 50 ILE cc_start: 0.8238 (mt) cc_final: 0.7964 (tt) REVERT: G 52 LEU cc_start: 0.8444 (mt) cc_final: 0.8225 (mm) REVERT: G 115 LEU cc_start: 0.8256 (tp) cc_final: 0.7993 (tt) REVERT: G 122 LEU cc_start: 0.8246 (mt) cc_final: 0.7954 (mp) REVERT: G 202 LYS cc_start: 0.7528 (mmtt) cc_final: 0.7288 (mmtt) REVERT: G 249 SER cc_start: 0.8214 (m) cc_final: 0.7998 (p) outliers start: 33 outliers final: 22 residues processed: 405 average time/residue: 0.1171 time to fit residues: 69.8150 Evaluate side-chains 409 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 381 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 271 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 25 optimal weight: 3.9990 chunk 88 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 chunk 154 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 133 optimal weight: 0.5980 chunk 147 optimal weight: 0.7980 chunk 163 optimal weight: 0.8980 chunk 134 optimal weight: 0.7980 chunk 136 optimal weight: 0.3980 chunk 92 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 ASN F 337 ASN G 100 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.148476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.133647 restraints weight = 18914.518| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.87 r_work: 0.3593 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14791 Z= 0.122 Angle : 0.499 7.936 20048 Z= 0.248 Chirality : 0.037 0.188 2373 Planarity : 0.003 0.039 2394 Dihedral : 3.564 19.184 1904 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.82 % Allowed : 17.63 % Favored : 80.55 % 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: 2.41 (0.20), residues: 1750 helix: 2.25 (0.14), residues: 1302 sheet: None (None), residues: 0 loop : -0.36 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 29 TYR 0.020 0.001 TYR A 212 PHE 0.014 0.001 PHE A 54 TRP 0.018 0.002 TRP F 104 HIS 0.005 0.001 HIS F 207 Details of bonding type rmsd covalent geometry : bond 0.00281 (14791) covalent geometry : angle 0.49919 (20048) hydrogen bonds : bond 0.03477 ( 991) hydrogen bonds : angle 3.75332 ( 2892) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 390 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8445 (tp) cc_final: 0.8093 (tp) REVERT: A 50 ILE cc_start: 0.8216 (mt) cc_final: 0.7920 (tt) REVERT: A 51 SER cc_start: 0.8013 (m) cc_final: 0.7738 (p) REVERT: A 228 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8113 (mt) REVERT: A 231 SER cc_start: 0.8440 (t) cc_final: 0.8216 (m) REVERT: A 233 TYR cc_start: 0.8386 (t80) cc_final: 0.8177 (t80) REVERT: A 234 PHE cc_start: 0.8600 (t80) cc_final: 0.8156 (t80) REVERT: A 274 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7704 (mp) REVERT: B 228 ILE cc_start: 0.8430 (tp) cc_final: 0.8130 (tp) REVERT: B 271 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.8088 (tt) REVERT: B 349 VAL cc_start: 0.7041 (t) cc_final: 0.6789 (m) REVERT: C 52 LEU cc_start: 0.8383 (mm) cc_final: 0.8156 (mp) REVERT: C 106 HIS cc_start: 0.8247 (m-70) cc_final: 0.7942 (m90) REVERT: C 198 TYR cc_start: 0.7847 (t80) cc_final: 0.7583 (t80) REVERT: C 234 PHE cc_start: 0.8643 (t80) cc_final: 0.8284 (t80) REVERT: D 36 LYS cc_start: 0.8616 (tmtt) cc_final: 0.8060 (tmtt) REVERT: D 37 MET cc_start: 0.7946 (tpt) cc_final: 0.7579 (tpt) REVERT: D 52 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8350 (mp) REVERT: D 203 LYS cc_start: 0.8243 (tmmt) cc_final: 0.7903 (tmmt) REVERT: E 36 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8383 (tmtt) REVERT: E 50 ILE cc_start: 0.8140 (mt) cc_final: 0.7834 (tt) REVERT: E 51 SER cc_start: 0.8109 (m) cc_final: 0.7773 (p) REVERT: E 56 GLN cc_start: 0.6651 (OUTLIER) cc_final: 0.6353 (mm-40) REVERT: E 108 PHE cc_start: 0.8214 (m-80) cc_final: 0.7859 (m-80) REVERT: E 203 LYS cc_start: 0.8197 (tmmt) cc_final: 0.7884 (ttpp) REVERT: E 253 LYS cc_start: 0.8737 (ttmm) cc_final: 0.8501 (ttmm) REVERT: F 36 LYS cc_start: 0.8607 (tmtt) cc_final: 0.8284 (tmtt) REVERT: F 37 MET cc_start: 0.8236 (tpt) cc_final: 0.7845 (tpt) REVERT: F 83 TYR cc_start: 0.8230 (t80) cc_final: 0.7881 (t80) REVERT: F 249 SER cc_start: 0.8366 (m) cc_final: 0.8060 (p) REVERT: F 271 ILE cc_start: 0.8615 (mm) cc_final: 0.8188 (tp) REVERT: G 50 ILE cc_start: 0.8247 (mt) cc_final: 0.7982 (tt) REVERT: G 115 LEU cc_start: 0.8302 (tp) cc_final: 0.8045 (tt) REVERT: G 122 LEU cc_start: 0.8285 (mt) cc_final: 0.7997 (mp) REVERT: G 202 LYS cc_start: 0.7568 (mmtt) cc_final: 0.7346 (mmtt) outliers start: 30 outliers final: 22 residues processed: 403 average time/residue: 0.1234 time to fit residues: 72.8423 Evaluate side-chains 413 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 385 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 337 ASN Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 271 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 138 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 117 optimal weight: 0.4980 chunk 31 optimal weight: 0.0570 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS ** A 337 ASN ** 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 = 0.3906 r_free = 0.3906 target = 0.151831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.137213 restraints weight = 18840.496| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.91 r_work: 0.3586 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14791 Z= 0.136 Angle : 0.522 9.073 20048 Z= 0.258 Chirality : 0.037 0.184 2373 Planarity : 0.003 0.039 2394 Dihedral : 3.596 19.227 1904 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.70 % Allowed : 18.36 % Favored : 79.94 % 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: 2.37 (0.20), residues: 1750 helix: 2.22 (0.14), residues: 1302 sheet: None (None), residues: 0 loop : -0.37 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 75 TYR 0.036 0.002 TYR B 198 PHE 0.015 0.001 PHE A 54 TRP 0.020 0.002 TRP F 104 HIS 0.005 0.001 HIS F 207 Details of bonding type rmsd covalent geometry : bond 0.00318 (14791) covalent geometry : angle 0.52169 (20048) hydrogen bonds : bond 0.03574 ( 991) hydrogen bonds : angle 3.79468 ( 2892) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 390 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8414 (tp) cc_final: 0.7936 (tp) REVERT: A 50 ILE cc_start: 0.8201 (mt) cc_final: 0.7908 (tt) REVERT: A 51 SER cc_start: 0.8060 (m) cc_final: 0.7742 (p) REVERT: A 228 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.8088 (mt) REVERT: A 231 SER cc_start: 0.8451 (t) cc_final: 0.8230 (m) REVERT: A 234 PHE cc_start: 0.8627 (t80) cc_final: 0.8116 (t80) REVERT: A 274 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7702 (mp) REVERT: B 228 ILE cc_start: 0.8438 (tp) cc_final: 0.8133 (tp) REVERT: B 271 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.8064 (tt) REVERT: B 349 VAL cc_start: 0.7037 (t) cc_final: 0.6762 (m) REVERT: C 52 LEU cc_start: 0.8328 (mm) cc_final: 0.8091 (mp) REVERT: C 106 HIS cc_start: 0.8234 (m-70) cc_final: 0.7928 (m90) REVERT: C 198 TYR cc_start: 0.7848 (t80) cc_final: 0.7578 (t80) REVERT: C 234 PHE cc_start: 0.8684 (t80) cc_final: 0.8283 (t80) REVERT: D 36 LYS cc_start: 0.8609 (tmtt) cc_final: 0.8020 (tmtt) REVERT: D 37 MET cc_start: 0.7938 (tpt) cc_final: 0.7557 (tpt) REVERT: D 52 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8318 (mp) REVERT: D 203 LYS cc_start: 0.8183 (tmmt) cc_final: 0.7817 (tmmt) REVERT: E 36 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8372 (tmtt) REVERT: E 50 ILE cc_start: 0.8226 (mt) cc_final: 0.7926 (tt) REVERT: E 51 SER cc_start: 0.8137 (m) cc_final: 0.7771 (p) REVERT: E 56 GLN cc_start: 0.6649 (OUTLIER) cc_final: 0.6385 (mm-40) REVERT: E 108 PHE cc_start: 0.8260 (m-80) cc_final: 0.7921 (m-80) REVERT: E 203 LYS cc_start: 0.8197 (tmmt) cc_final: 0.7875 (ttpp) REVERT: E 253 LYS cc_start: 0.8736 (ttmm) cc_final: 0.8481 (ttmm) REVERT: F 36 LYS cc_start: 0.8598 (tmtt) cc_final: 0.8277 (tmtt) REVERT: F 37 MET cc_start: 0.8285 (tpt) cc_final: 0.7864 (tpt) REVERT: F 83 TYR cc_start: 0.8186 (t80) cc_final: 0.7767 (t80) REVERT: F 249 SER cc_start: 0.8352 (m) cc_final: 0.8023 (p) REVERT: F 271 ILE cc_start: 0.8609 (mm) cc_final: 0.8126 (tp) REVERT: G 50 ILE cc_start: 0.8242 (mt) cc_final: 0.7989 (tt) REVERT: G 115 LEU cc_start: 0.8263 (tp) cc_final: 0.7998 (tt) REVERT: G 122 LEU cc_start: 0.8250 (mt) cc_final: 0.7990 (mp) REVERT: G 202 LYS cc_start: 0.7556 (mmtt) cc_final: 0.7320 (mmtt) outliers start: 28 outliers final: 21 residues processed: 403 average time/residue: 0.1255 time to fit residues: 73.5086 Evaluate side-chains 409 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 382 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 271 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 135 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 71 optimal weight: 0.0070 chunk 78 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.151869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.137151 restraints weight = 18898.834| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.92 r_work: 0.3586 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14791 Z= 0.133 Angle : 0.522 10.754 20048 Z= 0.257 Chirality : 0.037 0.184 2373 Planarity : 0.003 0.039 2394 Dihedral : 3.605 19.251 1904 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.88 % Allowed : 18.30 % Favored : 79.82 % 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: 2.34 (0.20), residues: 1750 helix: 2.20 (0.14), residues: 1302 sheet: None (None), residues: 0 loop : -0.41 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 29 TYR 0.028 0.001 TYR B 198 PHE 0.015 0.001 PHE F 295 TRP 0.021 0.002 TRP F 104 HIS 0.005 0.001 HIS F 207 Details of bonding type rmsd covalent geometry : bond 0.00310 (14791) covalent geometry : angle 0.52173 (20048) hydrogen bonds : bond 0.03597 ( 991) hydrogen bonds : angle 3.81802 ( 2892) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3425.92 seconds wall clock time: 59 minutes 43.45 seconds (3583.45 seconds total)