Starting phenix.real_space_refine on Tue Mar 3 22:10:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wco_32426/03_2026/7wco_32426.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wco_32426/03_2026/7wco_32426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wco_32426/03_2026/7wco_32426.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wco_32426/03_2026/7wco_32426.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wco_32426/03_2026/7wco_32426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wco_32426/03_2026/7wco_32426.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 80 5.16 5 C 5670 2.51 5 N 1585 2.21 5 O 1615 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s 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: 8950 Number of models: 1 Model: "" Number of chains: 3 Chain: "J" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 203 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "K" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 366 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "L" Number of atoms: 1221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1221 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 149} Restraints were copied for chains: A, D, G, M, B, E, H, N, C, F, I, O Time building chain proxies: 1.13, per 1000 atoms: 0.13 Number of scatterers: 8950 At special positions: 0 Unit cell: (119.68, 116.96, 95.2, 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 80 16.00 O 1615 8.00 N 1585 7.00 C 5670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 351.1 milliseconds 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2150 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 20 sheets defined 33.9% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'J' and resid 412 through 435 removed outlier: 3.674A pdb=" N LEU J 417 " --> pdb=" O VAL J 413 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY J 418 " --> pdb=" O ALA J 414 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU J 422 " --> pdb=" O GLY J 418 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA J 423 " --> pdb=" O GLY J 419 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU J 430 " --> pdb=" O ALA J 426 " (cutoff:3.500A) Processing helix chain 'K' and resid 372 through 377 Processing helix chain 'K' and resid 377 through 382 Processing helix chain 'K' and resid 382 through 402 removed outlier: 3.831A pdb=" N PHE K 388 " --> pdb=" O SER K 384 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA K 391 " --> pdb=" O MET K 387 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS K 395 " --> pdb=" O ALA K 391 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU K 396 " --> pdb=" O ARG K 392 " (cutoff:3.500A) Proline residue: K 398 - end of helix removed outlier: 3.687A pdb=" N LEU K 401 " --> pdb=" O THR K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 407 through 414 removed outlier: 3.628A pdb=" N LEU K 411 " --> pdb=" O VAL K 407 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 121 removed outlier: 3.554A pdb=" N GLU L 117 " --> pdb=" O MET L 114 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN L 118 " --> pdb=" O LYS L 115 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP L 119 " --> pdb=" O ILE L 116 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE L 121 " --> pdb=" O ASN L 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 175 through 182 removed outlier: 3.574A pdb=" N LYS L 179 " --> pdb=" O VAL L 176 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N SER L 180 " --> pdb=" O HIS L 177 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP L 181 " --> pdb=" O MET L 178 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA L 182 " --> pdb=" O LYS L 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 435 removed outlier: 3.674A pdb=" N LEU A 417 " --> pdb=" O VAL A 413 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU A 422 " --> pdb=" O GLY A 418 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 423 " --> pdb=" O GLY A 419 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU A 430 " --> pdb=" O ALA A 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 Processing helix chain 'B' and resid 377 through 382 Processing helix chain 'B' and resid 382 through 402 removed outlier: 3.831A pdb=" N PHE B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA B 391 " --> pdb=" O MET B 387 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) Proline residue: B 398 - end of helix removed outlier: 3.687A pdb=" N LEU B 401 " --> pdb=" O THR B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 414 removed outlier: 3.628A pdb=" N LEU B 411 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 121 removed outlier: 3.553A pdb=" N GLU C 117 " --> pdb=" O MET C 114 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN C 118 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP C 119 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE C 121 " --> pdb=" O ASN C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 182 removed outlier: 3.574A pdb=" N LYS C 179 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N SER C 180 " --> pdb=" O HIS C 177 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP C 181 " --> pdb=" O MET C 178 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA C 182 " --> pdb=" O LYS C 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 435 removed outlier: 3.674A pdb=" N LEU D 417 " --> pdb=" O VAL D 413 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY D 418 " --> pdb=" O ALA D 414 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU D 422 " --> pdb=" O GLY D 418 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 423 " --> pdb=" O GLY D 419 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU D 430 " --> pdb=" O ALA D 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 377 Processing helix chain 'E' and resid 377 through 382 Processing helix chain 'E' and resid 382 through 402 removed outlier: 3.831A pdb=" N PHE E 388 " --> pdb=" O SER E 384 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA E 391 " --> pdb=" O MET E 387 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS E 395 " --> pdb=" O ALA E 391 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) Proline residue: E 398 - end of helix removed outlier: 3.687A pdb=" N LEU E 401 " --> pdb=" O THR E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 414 removed outlier: 3.629A pdb=" N LEU E 411 " --> pdb=" O VAL E 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 121 removed outlier: 3.553A pdb=" N GLU F 117 " --> pdb=" O MET F 114 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN F 118 " --> pdb=" O LYS F 115 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP F 119 " --> pdb=" O ILE F 116 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE F 121 " --> pdb=" O ASN F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 182 removed outlier: 3.573A pdb=" N LYS F 179 " --> pdb=" O VAL F 176 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N SER F 180 " --> pdb=" O HIS F 177 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP F 181 " --> pdb=" O MET F 178 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA F 182 " --> pdb=" O LYS F 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 412 through 435 removed outlier: 3.674A pdb=" N LEU G 417 " --> pdb=" O VAL G 413 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY G 418 " --> pdb=" O ALA G 414 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU G 422 " --> pdb=" O GLY G 418 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA G 423 " --> pdb=" O GLY G 419 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU G 430 " --> pdb=" O ALA G 426 " (cutoff:3.500A) Processing helix chain 'H' and resid 372 through 377 Processing helix chain 'H' and resid 377 through 382 Processing helix chain 'H' and resid 382 through 402 removed outlier: 3.831A pdb=" N PHE H 388 " --> pdb=" O SER H 384 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA H 391 " --> pdb=" O MET H 387 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS H 395 " --> pdb=" O ALA H 391 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU H 396 " --> pdb=" O ARG H 392 " (cutoff:3.500A) Proline residue: H 398 - end of helix removed outlier: 3.687A pdb=" N LEU H 401 " --> pdb=" O THR H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 407 through 414 removed outlier: 3.629A pdb=" N LEU H 411 " --> pdb=" O VAL H 407 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 121 removed outlier: 3.554A pdb=" N GLU I 117 " --> pdb=" O MET I 114 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN I 118 " --> pdb=" O LYS I 115 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP I 119 " --> pdb=" O ILE I 116 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE I 121 " --> pdb=" O ASN I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 175 through 182 removed outlier: 3.574A pdb=" N LYS I 179 " --> pdb=" O VAL I 176 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N SER I 180 " --> pdb=" O HIS I 177 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP I 181 " --> pdb=" O MET I 178 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA I 182 " --> pdb=" O LYS I 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 412 through 435 removed outlier: 3.674A pdb=" N LEU M 417 " --> pdb=" O VAL M 413 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY M 418 " --> pdb=" O ALA M 414 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU M 422 " --> pdb=" O GLY M 418 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA M 423 " --> pdb=" O GLY M 419 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU M 430 " --> pdb=" O ALA M 426 " (cutoff:3.500A) Processing helix chain 'N' and resid 372 through 377 Processing helix chain 'N' and resid 377 through 382 Processing helix chain 'N' and resid 382 through 402 removed outlier: 3.831A pdb=" N PHE N 388 " --> pdb=" O SER N 384 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA N 391 " --> pdb=" O MET N 387 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS N 395 " --> pdb=" O ALA N 391 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU N 396 " --> pdb=" O ARG N 392 " (cutoff:3.500A) Proline residue: N 398 - end of helix removed outlier: 3.687A pdb=" N LEU N 401 " --> pdb=" O THR N 397 " (cutoff:3.500A) Processing helix chain 'N' and resid 407 through 414 removed outlier: 3.628A pdb=" N LEU N 411 " --> pdb=" O VAL N 407 " (cutoff:3.500A) Processing helix chain 'O' and resid 114 through 121 removed outlier: 3.554A pdb=" N GLU O 117 " --> pdb=" O MET O 114 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN O 118 " --> pdb=" O LYS O 115 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP O 119 " --> pdb=" O ILE O 116 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE O 121 " --> pdb=" O ASN O 118 " (cutoff:3.500A) Processing helix chain 'O' and resid 175 through 182 removed outlier: 3.574A pdb=" N LYS O 179 " --> pdb=" O VAL O 176 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N SER O 180 " --> pdb=" O HIS O 177 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP O 181 " --> pdb=" O MET O 178 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA O 182 " --> pdb=" O LYS O 179 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'L' and resid 130 through 133 removed outlier: 7.196A pdb=" N VAL L 124 " --> pdb=" O THR L 131 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'L' and resid 184 through 185 removed outlier: 6.710A pdb=" N LYS L 184 " --> pdb=" O VAL L 231 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ALA L 233 " --> pdb=" O LYS L 184 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE L 224 " --> pdb=" O VAL L 232 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'L' and resid 193 through 194 removed outlier: 3.670A pdb=" N GLN L 202 " --> pdb=" O THR L 209 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'L' and resid 249 through 252 removed outlier: 3.530A pdb=" N THR L 251 " --> pdb=" O THR L 258 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'C' and resid 130 through 133 removed outlier: 7.195A pdb=" N VAL C 124 " --> pdb=" O THR C 131 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'C' and resid 184 through 185 removed outlier: 6.710A pdb=" N LYS C 184 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ALA C 233 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE C 224 " --> pdb=" O VAL C 232 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'C' and resid 193 through 194 removed outlier: 3.671A pdb=" N GLN C 202 " --> pdb=" O THR C 209 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'C' and resid 249 through 252 removed outlier: 3.530A pdb=" N THR C 251 " --> pdb=" O THR C 258 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'F' and resid 130 through 133 removed outlier: 7.196A pdb=" N VAL F 124 " --> pdb=" O THR F 131 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'F' and resid 184 through 185 removed outlier: 6.710A pdb=" N LYS F 184 " --> pdb=" O VAL F 231 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ALA F 233 " --> pdb=" O LYS F 184 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE F 224 " --> pdb=" O VAL F 232 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'F' and resid 193 through 194 removed outlier: 3.670A pdb=" N GLN F 202 " --> pdb=" O THR F 209 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'F' and resid 249 through 252 removed outlier: 3.530A pdb=" N THR F 251 " --> pdb=" O THR F 258 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'I' and resid 130 through 133 removed outlier: 7.196A pdb=" N VAL I 124 " --> pdb=" O THR I 131 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'I' and resid 184 through 185 removed outlier: 6.710A pdb=" N LYS I 184 " --> pdb=" O VAL I 231 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ALA I 233 " --> pdb=" O LYS I 184 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE I 224 " --> pdb=" O VAL I 232 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'I' and resid 193 through 194 removed outlier: 3.670A pdb=" N GLN I 202 " --> pdb=" O THR I 209 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'I' and resid 249 through 252 removed outlier: 3.530A pdb=" N THR I 251 " --> pdb=" O THR I 258 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'O' and resid 130 through 133 removed outlier: 7.196A pdb=" N VAL O 124 " --> pdb=" O THR O 131 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'O' and resid 184 through 185 removed outlier: 6.710A pdb=" N LYS O 184 " --> pdb=" O VAL O 231 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ALA O 233 " --> pdb=" O LYS O 184 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE O 224 " --> pdb=" O VAL O 232 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'O' and resid 193 through 194 removed outlier: 3.670A pdb=" N GLN O 202 " --> pdb=" O THR O 209 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'O' and resid 249 through 252 removed outlier: 3.530A pdb=" N THR O 251 " --> pdb=" O THR O 258 " (cutoff:3.500A) 235 hydrogen bonds defined for protein. 615 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: 1.23 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2875 1.34 - 1.46: 1979 1.46 - 1.58: 4156 1.58 - 1.70: 0 1.70 - 1.82: 115 Bond restraints: 9125 Sorted by residual: bond pdb=" N ALA H 420 " pdb=" CA ALA H 420 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.27e-02 6.20e+03 6.21e+00 bond pdb=" N ALA B 420 " pdb=" CA ALA B 420 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.27e-02 6.20e+03 6.06e+00 bond pdb=" N ALA K 420 " pdb=" CA ALA K 420 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.27e-02 6.20e+03 6.01e+00 bond pdb=" N ALA E 420 " pdb=" CA ALA E 420 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.27e-02 6.20e+03 5.91e+00 bond pdb=" N ALA N 420 " pdb=" CA ALA N 420 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.27e-02 6.20e+03 5.88e+00 ... (remaining 9120 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 11491 2.01 - 4.01: 739 4.01 - 6.02: 95 6.02 - 8.02: 20 8.02 - 10.03: 20 Bond angle restraints: 12365 Sorted by residual: angle pdb=" CA LYS F 158 " pdb=" CB LYS F 158 " pdb=" CG LYS F 158 " ideal model delta sigma weight residual 114.10 122.60 -8.50 2.00e+00 2.50e-01 1.81e+01 angle pdb=" CA LYS C 158 " pdb=" CB LYS C 158 " pdb=" CG LYS C 158 " ideal model delta sigma weight residual 114.10 122.60 -8.50 2.00e+00 2.50e-01 1.80e+01 angle pdb=" CA LYS L 158 " pdb=" CB LYS L 158 " pdb=" CG LYS L 158 " ideal model delta sigma weight residual 114.10 122.60 -8.50 2.00e+00 2.50e-01 1.80e+01 angle pdb=" CA LYS O 158 " pdb=" CB LYS O 158 " pdb=" CG LYS O 158 " ideal model delta sigma weight residual 114.10 122.59 -8.49 2.00e+00 2.50e-01 1.80e+01 angle pdb=" CA LYS I 158 " pdb=" CB LYS I 158 " pdb=" CG LYS I 158 " ideal model delta sigma weight residual 114.10 122.56 -8.46 2.00e+00 2.50e-01 1.79e+01 ... (remaining 12360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 5185 17.02 - 34.04: 195 34.04 - 51.06: 75 51.06 - 68.07: 0 68.07 - 85.09: 5 Dihedral angle restraints: 5460 sinusoidal: 2085 harmonic: 3375 Sorted by residual: dihedral pdb=" CA ARG H 419 " pdb=" C ARG H 419 " pdb=" N ALA H 420 " pdb=" CA ALA H 420 " ideal model delta harmonic sigma weight residual 180.00 131.29 48.71 0 5.00e+00 4.00e-02 9.49e+01 dihedral pdb=" CA ARG K 419 " pdb=" C ARG K 419 " pdb=" N ALA K 420 " pdb=" CA ALA K 420 " ideal model delta harmonic sigma weight residual 180.00 131.31 48.69 0 5.00e+00 4.00e-02 9.48e+01 dihedral pdb=" CA ARG B 419 " pdb=" C ARG B 419 " pdb=" N ALA B 420 " pdb=" CA ALA B 420 " ideal model delta harmonic sigma weight residual 180.00 131.31 48.69 0 5.00e+00 4.00e-02 9.48e+01 ... (remaining 5457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 953 0.054 - 0.108: 368 0.108 - 0.162: 87 0.162 - 0.216: 17 0.216 - 0.270: 10 Chirality restraints: 1435 Sorted by residual: chirality pdb=" CA THR B 397 " pdb=" N THR B 397 " pdb=" C THR B 397 " pdb=" CB THR B 397 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA THR H 397 " pdb=" N THR H 397 " pdb=" C THR H 397 " pdb=" CB THR H 397 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA THR N 397 " pdb=" N THR N 397 " pdb=" C THR N 397 " pdb=" CB THR N 397 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1432 not shown) Planarity restraints: 1555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 435 " -0.030 2.00e-02 2.50e+03 5.80e-02 3.36e+01 pdb=" C THR D 435 " 0.100 2.00e-02 2.50e+03 pdb=" O THR D 435 " -0.037 2.00e-02 2.50e+03 pdb=" N MET D 436 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 435 " -0.030 2.00e-02 2.50e+03 5.80e-02 3.36e+01 pdb=" C THR G 435 " 0.100 2.00e-02 2.50e+03 pdb=" O THR G 435 " -0.037 2.00e-02 2.50e+03 pdb=" N MET G 436 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR J 435 " -0.030 2.00e-02 2.50e+03 5.79e-02 3.35e+01 pdb=" C THR J 435 " 0.100 2.00e-02 2.50e+03 pdb=" O THR J 435 " -0.037 2.00e-02 2.50e+03 pdb=" N MET J 436 " -0.033 2.00e-02 2.50e+03 ... (remaining 1552 not shown) Histogram of nonbonded interaction distances: 0.60 - 1.46: 45 1.46 - 2.32: 80 2.32 - 3.18: 7375 3.18 - 4.04: 20488 4.04 - 4.90: 36824 Warning: very small nonbonded interaction distances. Nonbonded interactions: 64812 Sorted by model distance: nonbonded pdb=" CD1 LEU K 411 " pdb=" CZ ARG A 437 " model vdw 0.599 3.690 nonbonded pdb=" CD1 LEU H 411 " pdb=" CZ ARG M 437 " model vdw 0.599 3.690 nonbonded pdb=" CD1 LEU B 411 " pdb=" CZ ARG D 437 " model vdw 0.600 3.690 nonbonded pdb=" CZ ARG J 437 " pdb=" CD1 LEU N 411 " model vdw 0.600 3.690 nonbonded pdb=" CD1 LEU E 411 " pdb=" CZ ARG G 437 " model vdw 0.600 3.690 ... (remaining 64807 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: 0.03 Found NCS groups: ncs_group { reference = chain 'J' selection = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'M' } ncs_group { reference = chain 'K' selection = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'N' } ncs_group { reference = chain 'L' selection = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.020 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 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 : 0.008 0.090 9125 Z= 0.359 Angle : 1.133 10.027 12365 Z= 0.617 Chirality : 0.063 0.270 1435 Planarity : 0.011 0.082 1555 Dihedral : 11.024 85.092 3310 Min Nonbonded Distance : 0.599 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.16 % Favored : 85.84 % Rotamer: Outliers : 0.53 % Allowed : 7.41 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.89 % 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: -5.43 (0.18), residues: 1165 helix: -4.70 (0.11), residues: 300 sheet: -3.60 (0.36), residues: 120 loop : -3.29 (0.19), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 259 TYR 0.025 0.003 TYR I 161 PHE 0.012 0.002 PHE C 208 TRP 0.044 0.004 TRP C 196 HIS 0.009 0.002 HIS F 146 Details of bonding type rmsd covalent geometry : bond 0.00808 ( 9125) covalent geometry : angle 1.13291 (12365) hydrogen bonds : bond 0.32690 ( 235) hydrogen bonds : angle 11.06485 ( 615) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 357 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7698 (mtt180) cc_final: 0.6632 (mtm-85) REVERT: K 387 MET cc_start: 0.8317 (mtt) cc_final: 0.8109 (mtp) REVERT: K 394 LYS cc_start: 0.9341 (ttmt) cc_final: 0.8945 (ttmm) REVERT: K 415 CYS cc_start: 0.8340 (m) cc_final: 0.8100 (m) REVERT: L 126 LEU cc_start: 0.8053 (pt) cc_final: 0.7846 (tp) REVERT: L 235 VAL cc_start: 0.9695 (t) cc_final: 0.9457 (p) REVERT: A 412 ARG cc_start: 0.7636 (mtt180) cc_final: 0.6776 (mtm-85) REVERT: B 387 MET cc_start: 0.8243 (mtt) cc_final: 0.8029 (mtp) REVERT: B 394 LYS cc_start: 0.9361 (ttmt) cc_final: 0.9000 (ttmm) REVERT: C 133 TYR cc_start: 0.8833 (m-80) cc_final: 0.8623 (m-80) REVERT: C 135 CYS cc_start: 0.8901 (t) cc_final: 0.8645 (t) REVERT: C 168 ASP cc_start: 0.8756 (t70) cc_final: 0.8300 (t0) REVERT: C 235 VAL cc_start: 0.9735 (t) cc_final: 0.9480 (p) REVERT: D 412 ARG cc_start: 0.7585 (mtt180) cc_final: 0.6356 (mtm-85) REVERT: E 394 LYS cc_start: 0.9418 (ttmt) cc_final: 0.9048 (ttmm) REVERT: F 112 MET cc_start: 0.7627 (ttm) cc_final: 0.7304 (mmm) REVERT: F 202 GLN cc_start: 0.8636 (pm20) cc_final: 0.8434 (pt0) REVERT: F 235 VAL cc_start: 0.9736 (t) cc_final: 0.9500 (p) REVERT: F 265 THR cc_start: 0.8921 (p) cc_final: 0.8562 (t) REVERT: F 266 GLU cc_start: 0.8000 (pm20) cc_final: 0.7653 (pm20) REVERT: G 412 ARG cc_start: 0.7570 (mtt180) cc_final: 0.6473 (mtm-85) REVERT: H 386 TYR cc_start: 0.9010 (t80) cc_final: 0.8601 (t80) REVERT: H 387 MET cc_start: 0.8312 (mtt) cc_final: 0.8080 (mtp) REVERT: H 394 LYS cc_start: 0.9420 (ttmt) cc_final: 0.9029 (ttmm) REVERT: I 136 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8764 (tt) REVERT: I 161 TYR cc_start: 0.7971 (p90) cc_final: 0.7566 (p90) REVERT: I 168 ASP cc_start: 0.8841 (t70) cc_final: 0.8630 (t0) REVERT: I 185 TYR cc_start: 0.9202 (p90) cc_final: 0.8962 (p90) REVERT: I 266 GLU cc_start: 0.7898 (pm20) cc_final: 0.7398 (pm20) REVERT: M 412 ARG cc_start: 0.7641 (mtt180) cc_final: 0.7022 (mpp-170) REVERT: N 386 TYR cc_start: 0.9146 (t80) cc_final: 0.8713 (t80) REVERT: N 388 PHE cc_start: 0.8612 (m-10) cc_final: 0.8406 (m-10) REVERT: N 394 LYS cc_start: 0.9285 (ttmt) cc_final: 0.9046 (ttmm) REVERT: N 415 CYS cc_start: 0.7679 (m) cc_final: 0.7440 (m) REVERT: O 112 MET cc_start: 0.7646 (ttm) cc_final: 0.7117 (mmm) REVERT: O 133 TYR cc_start: 0.8830 (m-80) cc_final: 0.8614 (m-80) REVERT: O 136 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8659 (tt) REVERT: O 142 MET cc_start: 0.8781 (mtt) cc_final: 0.8560 (mtt) REVERT: O 161 TYR cc_start: 0.8101 (p90) cc_final: 0.7640 (p90) REVERT: O 204 SER cc_start: 0.9172 (t) cc_final: 0.8621 (p) REVERT: O 266 GLU cc_start: 0.7870 (pm20) cc_final: 0.7580 (pm20) outliers start: 5 outliers final: 0 residues processed: 362 average time/residue: 0.0979 time to fit residues: 47.3885 Evaluate side-chains 298 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 296 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain O residue 136 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 20.0000 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 202 GLN C 193 HIS C 202 GLN F 202 GLN I 202 GLN O 202 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.127732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.112265 restraints weight = 15005.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.115369 restraints weight = 7778.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.117487 restraints weight = 4873.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.118955 restraints weight = 3453.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.120009 restraints weight = 2670.950| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9125 Z= 0.153 Angle : 0.695 8.351 12365 Z= 0.366 Chirality : 0.047 0.234 1435 Planarity : 0.009 0.068 1555 Dihedral : 7.824 78.018 1294 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 4.97 % Allowed : 16.30 % Favored : 78.73 % 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: -4.75 (0.20), residues: 1165 helix: -3.32 (0.19), residues: 320 sheet: -3.24 (0.42), residues: 120 loop : -3.21 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG M 437 TYR 0.021 0.002 TYR I 133 PHE 0.008 0.001 PHE E 388 TRP 0.018 0.002 TRP I 196 HIS 0.004 0.001 HIS C 193 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9125) covalent geometry : angle 0.69491 (12365) hydrogen bonds : bond 0.04239 ( 235) hydrogen bonds : angle 5.60019 ( 615) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 344 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7512 (mtt180) cc_final: 0.6797 (mpp-170) REVERT: K 387 MET cc_start: 0.8278 (mtt) cc_final: 0.7983 (mtp) REVERT: K 394 LYS cc_start: 0.9297 (ttmt) cc_final: 0.8804 (ttmm) REVERT: L 142 MET cc_start: 0.8578 (mtt) cc_final: 0.8364 (mtp) REVERT: L 186 THR cc_start: 0.9122 (t) cc_final: 0.8834 (m) REVERT: L 204 SER cc_start: 0.9287 (t) cc_final: 0.8538 (p) REVERT: L 235 VAL cc_start: 0.9717 (t) cc_final: 0.9496 (p) REVERT: A 412 ARG cc_start: 0.7624 (mtt180) cc_final: 0.6933 (mpp-170) REVERT: B 387 MET cc_start: 0.8206 (mtt) cc_final: 0.7891 (mtp) REVERT: B 394 LYS cc_start: 0.9335 (ttmt) cc_final: 0.8902 (ttmm) REVERT: C 112 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.7080 (tpp) REVERT: C 133 TYR cc_start: 0.8804 (m-80) cc_final: 0.8601 (m-80) REVERT: C 135 CYS cc_start: 0.8812 (t) cc_final: 0.8581 (t) REVERT: C 168 ASP cc_start: 0.8848 (t70) cc_final: 0.8614 (t70) REVERT: C 186 THR cc_start: 0.9228 (OUTLIER) cc_final: 0.8913 (m) REVERT: C 265 THR cc_start: 0.8777 (p) cc_final: 0.8258 (t) REVERT: D 412 ARG cc_start: 0.7548 (mtt180) cc_final: 0.6633 (mpp-170) REVERT: E 394 LYS cc_start: 0.9409 (ttmt) cc_final: 0.8947 (ttmm) REVERT: F 153 ASN cc_start: 0.8967 (t0) cc_final: 0.8483 (t0) REVERT: F 156 LEU cc_start: 0.8614 (mp) cc_final: 0.8295 (mt) REVERT: F 168 ASP cc_start: 0.8744 (t70) cc_final: 0.8346 (t70) REVERT: F 204 SER cc_start: 0.9107 (t) cc_final: 0.8365 (p) REVERT: F 240 ASN cc_start: 0.9173 (t0) cc_final: 0.8936 (t0) REVERT: F 265 THR cc_start: 0.8858 (p) cc_final: 0.8591 (t) REVERT: G 412 ARG cc_start: 0.7670 (mtt180) cc_final: 0.6946 (mpp-170) REVERT: H 386 TYR cc_start: 0.8791 (t80) cc_final: 0.8421 (t80) REVERT: H 387 MET cc_start: 0.8342 (mtt) cc_final: 0.8131 (mtp) REVERT: H 394 LYS cc_start: 0.9302 (ttmt) cc_final: 0.8939 (ttmm) REVERT: I 152 ASP cc_start: 0.8044 (t0) cc_final: 0.7791 (t0) REVERT: I 168 ASP cc_start: 0.8929 (t70) cc_final: 0.8721 (t0) REVERT: I 185 TYR cc_start: 0.9208 (p90) cc_final: 0.9001 (p90) REVERT: I 204 SER cc_start: 0.9252 (t) cc_final: 0.8604 (p) REVERT: I 266 GLU cc_start: 0.7815 (pm20) cc_final: 0.7514 (pm20) REVERT: M 412 ARG cc_start: 0.7517 (mtt180) cc_final: 0.6832 (mpp-170) REVERT: N 394 LYS cc_start: 0.9315 (ttmt) cc_final: 0.9028 (ttmm) REVERT: O 204 SER cc_start: 0.9122 (t) cc_final: 0.8525 (p) REVERT: O 266 GLU cc_start: 0.7819 (pm20) cc_final: 0.7541 (pm20) REVERT: O 268 TRP cc_start: 0.8839 (m-10) cc_final: 0.8428 (m-10) outliers start: 47 outliers final: 20 residues processed: 367 average time/residue: 0.0967 time to fit residues: 47.5501 Evaluate side-chains 332 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 310 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 425 VAL Chi-restraints excluded: chain L residue 119 ASP Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain M residue 425 VAL Chi-restraints excluded: chain O residue 119 ASP Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 158 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 34 optimal weight: 0.6980 chunk 107 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 96 optimal weight: 0.7980 chunk 42 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 0.0070 chunk 12 optimal weight: 0.0670 chunk 37 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.130976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.115428 restraints weight = 14457.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.118553 restraints weight = 7426.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.120745 restraints weight = 4609.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.122260 restraints weight = 3226.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.123345 restraints weight = 2460.766| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9125 Z= 0.110 Angle : 0.622 7.651 12365 Z= 0.316 Chirality : 0.044 0.158 1435 Planarity : 0.007 0.060 1555 Dihedral : 7.032 81.527 1292 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 4.97 % Allowed : 17.99 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.04 (0.21), residues: 1165 helix: -2.31 (0.23), residues: 355 sheet: -2.90 (0.42), residues: 120 loop : -2.96 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 393 TYR 0.019 0.002 TYR N 386 PHE 0.007 0.001 PHE B 388 TRP 0.015 0.001 TRP O 196 HIS 0.002 0.001 HIS F 177 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 9125) covalent geometry : angle 0.62198 (12365) hydrogen bonds : bond 0.02944 ( 235) hydrogen bonds : angle 4.92226 ( 615) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 327 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7405 (mtt180) cc_final: 0.6703 (mpp-170) REVERT: K 394 LYS cc_start: 0.9367 (ttmt) cc_final: 0.8908 (ttmm) REVERT: L 112 MET cc_start: 0.7630 (tpt) cc_final: 0.7359 (tpp) REVERT: L 135 CYS cc_start: 0.8853 (t) cc_final: 0.8560 (t) REVERT: L 175 PRO cc_start: 0.9329 (Cg_exo) cc_final: 0.9083 (Cg_endo) REVERT: L 186 THR cc_start: 0.9162 (t) cc_final: 0.8941 (m) REVERT: B 387 MET cc_start: 0.8089 (mtt) cc_final: 0.7870 (mtp) REVERT: B 394 LYS cc_start: 0.9298 (ttmt) cc_final: 0.8853 (ttmm) REVERT: C 112 MET cc_start: 0.7370 (ttp) cc_final: 0.7109 (tpp) REVERT: C 136 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8527 (tt) REVERT: C 168 ASP cc_start: 0.8798 (t70) cc_final: 0.8245 (t70) REVERT: C 186 THR cc_start: 0.9224 (OUTLIER) cc_final: 0.8947 (m) REVERT: C 265 THR cc_start: 0.8786 (p) cc_final: 0.8292 (t) REVERT: D 412 ARG cc_start: 0.7643 (mtt180) cc_final: 0.6739 (mpp-170) REVERT: E 394 LYS cc_start: 0.9360 (ttmt) cc_final: 0.8883 (ttmm) REVERT: F 156 LEU cc_start: 0.8424 (mp) cc_final: 0.8157 (mp) REVERT: F 168 ASP cc_start: 0.8856 (t70) cc_final: 0.8445 (t70) REVERT: F 186 THR cc_start: 0.9188 (t) cc_final: 0.8950 (m) REVERT: F 189 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8663 (pttm) REVERT: F 204 SER cc_start: 0.8741 (t) cc_final: 0.7979 (p) REVERT: F 216 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.9094 (ttmm) REVERT: F 265 THR cc_start: 0.8699 (p) cc_final: 0.8301 (t) REVERT: G 412 ARG cc_start: 0.7508 (mtt180) cc_final: 0.6874 (mpp-170) REVERT: H 386 TYR cc_start: 0.8702 (t80) cc_final: 0.8332 (t80) REVERT: H 394 LYS cc_start: 0.9179 (ttmt) cc_final: 0.8845 (ttmm) REVERT: I 152 ASP cc_start: 0.8073 (t0) cc_final: 0.7811 (t0) REVERT: I 204 SER cc_start: 0.9245 (t) cc_final: 0.8647 (p) REVERT: I 240 ASN cc_start: 0.8933 (t0) cc_final: 0.8716 (t0) REVERT: I 266 GLU cc_start: 0.7708 (pm20) cc_final: 0.7352 (pm20) REVERT: N 388 PHE cc_start: 0.8354 (m-10) cc_final: 0.8119 (m-10) REVERT: N 394 LYS cc_start: 0.9369 (ttmt) cc_final: 0.9080 (ttmm) REVERT: O 133 TYR cc_start: 0.8935 (m-80) cc_final: 0.8729 (m-10) REVERT: O 136 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8367 (tt) REVERT: O 156 LEU cc_start: 0.8442 (mp) cc_final: 0.7655 (mp) REVERT: O 175 PRO cc_start: 0.9446 (Cg_exo) cc_final: 0.8961 (Cg_endo) REVERT: O 204 SER cc_start: 0.8993 (t) cc_final: 0.8332 (p) REVERT: O 240 ASN cc_start: 0.9023 (t0) cc_final: 0.8814 (t0) REVERT: O 266 GLU cc_start: 0.7755 (pm20) cc_final: 0.7540 (pm20) REVERT: O 268 TRP cc_start: 0.8771 (m-10) cc_final: 0.8405 (m-10) outliers start: 47 outliers final: 29 residues processed: 356 average time/residue: 0.0986 time to fit residues: 46.9073 Evaluate side-chains 338 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 304 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 425 VAL Chi-restraints excluded: chain J residue 437 ARG Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 189 LYS Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain G residue 437 ARG Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain M residue 425 VAL Chi-restraints excluded: chain M residue 437 ARG Chi-restraints excluded: chain N residue 411 LEU Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 158 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 5 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.123460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.108059 restraints weight = 14968.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.111058 restraints weight = 7575.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.113153 restraints weight = 4680.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.114599 restraints weight = 3296.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.115605 restraints weight = 2539.783| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9125 Z= 0.172 Angle : 0.670 10.629 12365 Z= 0.340 Chirality : 0.046 0.166 1435 Planarity : 0.007 0.061 1555 Dihedral : 6.742 75.070 1292 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 6.98 % Allowed : 22.22 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.77 (0.22), residues: 1165 helix: -1.62 (0.27), residues: 320 sheet: -2.73 (0.45), residues: 120 loop : -3.04 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 111 TYR 0.020 0.002 TYR F 161 PHE 0.009 0.001 PHE O 208 TRP 0.017 0.002 TRP I 196 HIS 0.003 0.001 HIS L 193 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 9125) covalent geometry : angle 0.66988 (12365) hydrogen bonds : bond 0.03655 ( 235) hydrogen bonds : angle 5.05636 ( 615) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 297 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7541 (mtt180) cc_final: 0.6832 (mpp-170) REVERT: J 417 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7412 (pp) REVERT: K 394 LYS cc_start: 0.9367 (ttmt) cc_final: 0.8930 (ttmm) REVERT: L 112 MET cc_start: 0.7713 (tpt) cc_final: 0.7401 (tpp) REVERT: L 186 THR cc_start: 0.9270 (t) cc_final: 0.8981 (m) REVERT: A 417 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7384 (pp) REVERT: B 387 MET cc_start: 0.8203 (mtt) cc_final: 0.7826 (mtp) REVERT: B 394 LYS cc_start: 0.9362 (ttmt) cc_final: 0.9015 (ttmm) REVERT: B 411 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7394 (tp) REVERT: C 136 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8654 (tt) REVERT: C 168 ASP cc_start: 0.8850 (t70) cc_final: 0.8218 (t0) REVERT: C 186 THR cc_start: 0.9317 (OUTLIER) cc_final: 0.9029 (m) REVERT: C 265 THR cc_start: 0.8864 (p) cc_final: 0.8309 (t) REVERT: C 268 TRP cc_start: 0.8799 (m-10) cc_final: 0.8552 (m-10) REVERT: D 412 ARG cc_start: 0.7748 (mtt180) cc_final: 0.6845 (mpp-170) REVERT: E 394 LYS cc_start: 0.9470 (ttmt) cc_final: 0.9067 (ttmm) REVERT: F 189 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.7732 (pmmt) REVERT: F 207 ARG cc_start: 0.8422 (ptm160) cc_final: 0.8161 (ptm160) REVERT: F 265 THR cc_start: 0.8867 (p) cc_final: 0.8570 (t) REVERT: G 412 ARG cc_start: 0.7483 (mtt180) cc_final: 0.6902 (mpp-170) REVERT: G 417 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7563 (pp) REVERT: H 386 TYR cc_start: 0.8854 (t80) cc_final: 0.8413 (t80) REVERT: H 394 LYS cc_start: 0.9381 (ttmt) cc_final: 0.8854 (ttmm) REVERT: I 204 SER cc_start: 0.9324 (t) cc_final: 0.8821 (p) REVERT: I 240 ASN cc_start: 0.9012 (t0) cc_final: 0.8781 (t0) REVERT: I 266 GLU cc_start: 0.7791 (pm20) cc_final: 0.7468 (pm20) REVERT: M 412 ARG cc_start: 0.7577 (mtt180) cc_final: 0.6888 (mpp-170) REVERT: N 394 LYS cc_start: 0.9370 (ttmt) cc_final: 0.9107 (ttmm) REVERT: O 204 SER cc_start: 0.9217 (t) cc_final: 0.8658 (p) REVERT: O 266 GLU cc_start: 0.7900 (pm20) cc_final: 0.7671 (pm20) outliers start: 66 outliers final: 48 residues processed: 341 average time/residue: 0.0959 time to fit residues: 44.0025 Evaluate side-chains 348 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 293 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 417 LEU Chi-restraints excluded: chain J residue 425 VAL Chi-restraints excluded: chain J residue 427 VAL Chi-restraints excluded: chain J residue 432 THR Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain L residue 119 ASP Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain L residue 171 CYS Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 189 LYS Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain G residue 427 VAL Chi-restraints excluded: chain G residue 432 THR Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain M residue 425 VAL Chi-restraints excluded: chain M residue 427 VAL Chi-restraints excluded: chain M residue 432 THR Chi-restraints excluded: chain M residue 437 ARG Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain N residue 411 LEU Chi-restraints excluded: chain O residue 119 ASP Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 158 LYS Chi-restraints excluded: chain O residue 248 SER Chi-restraints excluded: chain O residue 265 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 73 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 98 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.119716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.104514 restraints weight = 15020.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.107416 restraints weight = 7586.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.109395 restraints weight = 4715.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.110759 restraints weight = 3355.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.111783 restraints weight = 2615.567| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9125 Z= 0.253 Angle : 0.739 11.882 12365 Z= 0.378 Chirality : 0.049 0.183 1435 Planarity : 0.007 0.063 1555 Dihedral : 6.762 69.756 1292 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Rotamer: Outliers : 8.57 % Allowed : 22.22 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.77 (0.22), residues: 1165 helix: -1.49 (0.28), residues: 320 sheet: -2.35 (0.39), residues: 170 loop : -3.20 (0.21), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 437 TYR 0.022 0.002 TYR F 161 PHE 0.014 0.002 PHE O 208 TRP 0.014 0.002 TRP L 196 HIS 0.013 0.001 HIS F 146 Details of bonding type rmsd covalent geometry : bond 0.00604 ( 9125) covalent geometry : angle 0.73860 (12365) hydrogen bonds : bond 0.04222 ( 235) hydrogen bonds : angle 5.26422 ( 615) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 305 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7558 (mtt180) cc_final: 0.6856 (mpp-170) REVERT: J 417 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7628 (pp) REVERT: K 394 LYS cc_start: 0.9277 (ttmt) cc_final: 0.8862 (ttmm) REVERT: B 387 MET cc_start: 0.8168 (mtt) cc_final: 0.7816 (mtp) REVERT: B 394 LYS cc_start: 0.9314 (ttmt) cc_final: 0.8980 (ttmm) REVERT: B 411 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7307 (tp) REVERT: C 136 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8681 (tt) REVERT: C 168 ASP cc_start: 0.8925 (t70) cc_final: 0.8331 (t0) REVERT: C 265 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8307 (t) REVERT: D 412 ARG cc_start: 0.7777 (mtt180) cc_final: 0.6872 (mpp-170) REVERT: E 394 LYS cc_start: 0.9486 (ttmt) cc_final: 0.9099 (ttmm) REVERT: F 168 ASP cc_start: 0.8870 (t70) cc_final: 0.8598 (t0) REVERT: F 189 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.7696 (pmmt) REVERT: F 207 ARG cc_start: 0.8511 (ptm160) cc_final: 0.8213 (ptm160) REVERT: F 265 THR cc_start: 0.8987 (p) cc_final: 0.8647 (t) REVERT: F 266 GLU cc_start: 0.8055 (pm20) cc_final: 0.7782 (pm20) REVERT: G 412 ARG cc_start: 0.7567 (mtt180) cc_final: 0.6831 (mpp-170) REVERT: G 417 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7664 (pp) REVERT: H 386 TYR cc_start: 0.8972 (t80) cc_final: 0.8492 (t80) REVERT: H 394 LYS cc_start: 0.9372 (ttmt) cc_final: 0.8862 (ttmm) REVERT: I 112 MET cc_start: 0.7325 (tpt) cc_final: 0.7056 (tpp) REVERT: I 185 TYR cc_start: 0.9158 (p90) cc_final: 0.8703 (p90) REVERT: I 240 ASN cc_start: 0.9049 (t0) cc_final: 0.8849 (t0) REVERT: I 266 GLU cc_start: 0.7871 (pm20) cc_final: 0.7577 (pm20) REVERT: M 412 ARG cc_start: 0.7603 (mtt180) cc_final: 0.7025 (mpp-170) REVERT: N 394 LYS cc_start: 0.9382 (ttmt) cc_final: 0.9135 (ttmm) REVERT: O 147 VAL cc_start: 0.8680 (t) cc_final: 0.8465 (p) REVERT: O 266 GLU cc_start: 0.7939 (pm20) cc_final: 0.7696 (pm20) outliers start: 81 outliers final: 61 residues processed: 353 average time/residue: 0.0909 time to fit residues: 43.8285 Evaluate side-chains 361 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 294 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 417 LEU Chi-restraints excluded: chain J residue 425 VAL Chi-restraints excluded: chain J residue 427 VAL Chi-restraints excluded: chain J residue 432 THR Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain L residue 119 ASP Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain L residue 164 SER Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain L residue 171 CYS Chi-restraints excluded: chain L residue 216 LYS Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 164 SER Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 189 LYS Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain G residue 427 VAL Chi-restraints excluded: chain G residue 432 THR Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain M residue 425 VAL Chi-restraints excluded: chain M residue 427 VAL Chi-restraints excluded: chain M residue 432 THR Chi-restraints excluded: chain M residue 437 ARG Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain N residue 411 LEU Chi-restraints excluded: chain O residue 119 ASP Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 158 LYS Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain O residue 248 SER Chi-restraints excluded: chain O residue 258 THR Chi-restraints excluded: chain O residue 265 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 72 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 87 optimal weight: 0.3980 chunk 78 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 2 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.125502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.109560 restraints weight = 14687.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.112677 restraints weight = 7443.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.114842 restraints weight = 4623.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.116334 restraints weight = 3266.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.117399 restraints weight = 2530.554| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9125 Z= 0.123 Angle : 0.626 8.527 12365 Z= 0.319 Chirality : 0.045 0.184 1435 Planarity : 0.006 0.061 1555 Dihedral : 6.640 74.528 1292 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 5.61 % Allowed : 26.35 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.46 (0.23), residues: 1165 helix: -1.25 (0.28), residues: 330 sheet: -2.58 (0.47), residues: 120 loop : -2.91 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 437 TYR 0.020 0.001 TYR L 203 PHE 0.007 0.001 PHE H 388 TRP 0.011 0.001 TRP O 196 HIS 0.010 0.001 HIS F 146 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9125) covalent geometry : angle 0.62599 (12365) hydrogen bonds : bond 0.03242 ( 235) hydrogen bonds : angle 4.81438 ( 615) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 298 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7536 (mtt180) cc_final: 0.6791 (mpp-170) REVERT: J 417 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7271 (pp) REVERT: K 394 LYS cc_start: 0.9214 (ttmt) cc_final: 0.8807 (ttmm) REVERT: L 186 THR cc_start: 0.9286 (t) cc_final: 0.8998 (m) REVERT: L 203 TYR cc_start: 0.9090 (t80) cc_final: 0.8647 (t80) REVERT: A 436 MET cc_start: 0.8424 (tmm) cc_final: 0.7909 (tmm) REVERT: B 387 MET cc_start: 0.8031 (mtt) cc_final: 0.7671 (mtp) REVERT: B 388 PHE cc_start: 0.8453 (m-10) cc_final: 0.8197 (m-80) REVERT: B 394 LYS cc_start: 0.9256 (ttmt) cc_final: 0.8934 (ttmm) REVERT: C 136 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8537 (tt) REVERT: C 168 ASP cc_start: 0.8851 (t70) cc_final: 0.8251 (t70) REVERT: C 265 THR cc_start: 0.8811 (OUTLIER) cc_final: 0.8314 (t) REVERT: E 394 LYS cc_start: 0.9380 (ttmt) cc_final: 0.8952 (ttmm) REVERT: F 168 ASP cc_start: 0.8848 (t70) cc_final: 0.8447 (t0) REVERT: F 189 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8413 (pttm) REVERT: F 265 THR cc_start: 0.8809 (p) cc_final: 0.8314 (t) REVERT: F 266 GLU cc_start: 0.7979 (pm20) cc_final: 0.7740 (pm20) REVERT: G 412 ARG cc_start: 0.7472 (mtt180) cc_final: 0.6866 (mpp-170) REVERT: H 394 LYS cc_start: 0.9329 (ttmt) cc_final: 0.8786 (ttmm) REVERT: I 185 TYR cc_start: 0.9155 (p90) cc_final: 0.8765 (p90) REVERT: I 204 SER cc_start: 0.9236 (t) cc_final: 0.8773 (p) REVERT: I 240 ASN cc_start: 0.9035 (t0) cc_final: 0.8804 (t0) REVERT: I 266 GLU cc_start: 0.7789 (pm20) cc_final: 0.7355 (pm20) REVERT: M 412 ARG cc_start: 0.7580 (mtt180) cc_final: 0.6864 (mpp-170) REVERT: N 394 LYS cc_start: 0.9338 (ttmt) cc_final: 0.9083 (ttmm) REVERT: O 136 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8329 (tt) REVERT: O 175 PRO cc_start: 0.9375 (Cg_exo) cc_final: 0.9063 (Cg_endo) REVERT: O 186 THR cc_start: 0.9394 (t) cc_final: 0.9180 (m) REVERT: O 266 GLU cc_start: 0.7857 (pm20) cc_final: 0.7304 (pm20) outliers start: 53 outliers final: 37 residues processed: 325 average time/residue: 0.0934 time to fit residues: 41.4073 Evaluate side-chains 328 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 286 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 417 LEU Chi-restraints excluded: chain J residue 425 VAL Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 189 LYS Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain M residue 425 VAL Chi-restraints excluded: chain M residue 437 ARG Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain O residue 119 ASP Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 158 LYS Chi-restraints excluded: chain O residue 174 ILE Chi-restraints excluded: chain O residue 248 SER Chi-restraints excluded: chain O residue 265 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 51 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 83 optimal weight: 0.0030 chunk 58 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 109 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 overall best weight: 2.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.122855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.107093 restraints weight = 14853.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.110162 restraints weight = 7445.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.112293 restraints weight = 4577.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.113791 restraints weight = 3216.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.114836 restraints weight = 2474.481| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9125 Z= 0.143 Angle : 0.644 9.054 12365 Z= 0.324 Chirality : 0.046 0.174 1435 Planarity : 0.006 0.061 1555 Dihedral : 6.438 73.038 1292 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 6.24 % Allowed : 26.67 % Favored : 67.09 % 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: -3.34 (0.23), residues: 1165 helix: -1.15 (0.29), residues: 330 sheet: -2.57 (0.46), residues: 120 loop : -2.82 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 437 TYR 0.018 0.002 TYR L 203 PHE 0.007 0.001 PHE O 208 TRP 0.013 0.001 TRP C 268 HIS 0.008 0.001 HIS F 146 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9125) covalent geometry : angle 0.64396 (12365) hydrogen bonds : bond 0.03268 ( 235) hydrogen bonds : angle 4.74310 ( 615) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 298 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7541 (mtt180) cc_final: 0.6804 (mpp-170) REVERT: K 394 LYS cc_start: 0.9223 (ttmt) cc_final: 0.8817 (ttmm) REVERT: L 186 THR cc_start: 0.9314 (t) cc_final: 0.9028 (m) REVERT: L 203 TYR cc_start: 0.9109 (t80) cc_final: 0.8669 (t80) REVERT: A 436 MET cc_start: 0.8509 (tmm) cc_final: 0.8008 (tmm) REVERT: B 387 MET cc_start: 0.8020 (mtt) cc_final: 0.7640 (mtp) REVERT: B 388 PHE cc_start: 0.8456 (m-10) cc_final: 0.8196 (m-80) REVERT: B 394 LYS cc_start: 0.9268 (ttmt) cc_final: 0.8940 (ttmm) REVERT: C 136 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8536 (tt) REVERT: C 168 ASP cc_start: 0.8871 (t70) cc_final: 0.8299 (t70) REVERT: C 265 THR cc_start: 0.8811 (OUTLIER) cc_final: 0.8279 (t) REVERT: E 394 LYS cc_start: 0.9349 (ttmt) cc_final: 0.9010 (ttmm) REVERT: F 168 ASP cc_start: 0.8874 (t70) cc_final: 0.8525 (t0) REVERT: F 207 ARG cc_start: 0.8368 (ptm160) cc_final: 0.8150 (ptm160) REVERT: F 266 GLU cc_start: 0.7995 (pm20) cc_final: 0.7738 (pm20) REVERT: G 412 ARG cc_start: 0.7564 (mtt180) cc_final: 0.6811 (mpp-170) REVERT: H 386 TYR cc_start: 0.8886 (t80) cc_final: 0.8346 (t80) REVERT: H 394 LYS cc_start: 0.9331 (ttmt) cc_final: 0.8799 (ttmm) REVERT: I 112 MET cc_start: 0.7481 (tpt) cc_final: 0.7186 (tpp) REVERT: I 133 TYR cc_start: 0.8746 (m-80) cc_final: 0.8533 (m-80) REVERT: I 185 TYR cc_start: 0.9187 (p90) cc_final: 0.8806 (p90) REVERT: I 204 SER cc_start: 0.9204 (t) cc_final: 0.8701 (p) REVERT: I 240 ASN cc_start: 0.9054 (t0) cc_final: 0.8822 (t0) REVERT: I 266 GLU cc_start: 0.7788 (pm20) cc_final: 0.7484 (pm20) REVERT: M 412 ARG cc_start: 0.7565 (mtt180) cc_final: 0.6964 (mpp-170) REVERT: M 436 MET cc_start: 0.8311 (tmm) cc_final: 0.7808 (tmm) REVERT: N 386 TYR cc_start: 0.8927 (t80) cc_final: 0.8558 (t80) REVERT: N 394 LYS cc_start: 0.9361 (ttmt) cc_final: 0.9109 (ttmm) REVERT: O 136 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8326 (tt) REVERT: O 175 PRO cc_start: 0.9344 (Cg_exo) cc_final: 0.8903 (Cg_endo) REVERT: O 186 THR cc_start: 0.9438 (t) cc_final: 0.9223 (m) REVERT: O 266 GLU cc_start: 0.7873 (pm20) cc_final: 0.7622 (pm20) outliers start: 59 outliers final: 44 residues processed: 329 average time/residue: 0.0943 time to fit residues: 42.5030 Evaluate side-chains 341 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 294 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 425 VAL Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain L residue 164 SER Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain G residue 432 THR Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain M residue 425 VAL Chi-restraints excluded: chain M residue 437 ARG Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain N residue 411 LEU Chi-restraints excluded: chain O residue 116 ILE Chi-restraints excluded: chain O residue 119 ASP Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 158 LYS Chi-restraints excluded: chain O residue 248 SER Chi-restraints excluded: chain O residue 265 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 24 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 76 optimal weight: 0.0570 chunk 99 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.128102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.111874 restraints weight = 14609.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.115092 restraints weight = 7417.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.117328 restraints weight = 4591.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.118849 restraints weight = 3234.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.119920 restraints weight = 2495.184| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9125 Z= 0.114 Angle : 0.612 7.532 12365 Z= 0.308 Chirality : 0.045 0.166 1435 Planarity : 0.006 0.060 1555 Dihedral : 6.406 76.288 1292 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 4.44 % Allowed : 28.47 % Favored : 67.09 % 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: -3.13 (0.23), residues: 1165 helix: -1.03 (0.28), residues: 340 sheet: -2.56 (0.45), residues: 120 loop : -2.65 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 437 TYR 0.019 0.001 TYR I 133 PHE 0.004 0.001 PHE H 388 TRP 0.014 0.001 TRP C 268 HIS 0.007 0.001 HIS F 146 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9125) covalent geometry : angle 0.61180 (12365) hydrogen bonds : bond 0.02862 ( 235) hydrogen bonds : angle 4.48461 ( 615) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 297 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 394 LYS cc_start: 0.9195 (ttmt) cc_final: 0.8790 (ttmm) REVERT: L 186 THR cc_start: 0.9276 (t) cc_final: 0.8992 (m) REVERT: L 203 TYR cc_start: 0.9112 (t80) cc_final: 0.8721 (t80) REVERT: A 436 MET cc_start: 0.8199 (tmm) cc_final: 0.7964 (tmm) REVERT: B 388 PHE cc_start: 0.8433 (m-10) cc_final: 0.8162 (m-80) REVERT: B 394 LYS cc_start: 0.9223 (ttmt) cc_final: 0.8902 (ttmm) REVERT: C 136 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8527 (tt) REVERT: C 168 ASP cc_start: 0.8846 (t70) cc_final: 0.8269 (t70) REVERT: C 265 THR cc_start: 0.8723 (OUTLIER) cc_final: 0.8303 (t) REVERT: E 394 LYS cc_start: 0.9312 (ttmt) cc_final: 0.9008 (ttmm) REVERT: F 168 ASP cc_start: 0.8853 (t70) cc_final: 0.8523 (t0) REVERT: F 265 THR cc_start: 0.8684 (p) cc_final: 0.8253 (t) REVERT: F 266 GLU cc_start: 0.7946 (pm20) cc_final: 0.7703 (pm20) REVERT: G 412 ARG cc_start: 0.7439 (mtt180) cc_final: 0.6833 (mpp-170) REVERT: H 394 LYS cc_start: 0.9283 (ttmt) cc_final: 0.8856 (ttmm) REVERT: I 112 MET cc_start: 0.7303 (tpt) cc_final: 0.7067 (tpp) REVERT: I 123 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7627 (mt-10) REVERT: I 133 TYR cc_start: 0.8374 (m-80) cc_final: 0.7991 (m-80) REVERT: I 185 TYR cc_start: 0.9185 (p90) cc_final: 0.8820 (p90) REVERT: I 204 SER cc_start: 0.9128 (t) cc_final: 0.8629 (p) REVERT: I 240 ASN cc_start: 0.9041 (t0) cc_final: 0.8802 (t0) REVERT: I 266 GLU cc_start: 0.7770 (pm20) cc_final: 0.7380 (pm20) REVERT: M 412 ARG cc_start: 0.7548 (mtt180) cc_final: 0.6844 (mpp-170) REVERT: M 436 MET cc_start: 0.8225 (tmm) cc_final: 0.7751 (tmm) REVERT: N 388 PHE cc_start: 0.8185 (m-80) cc_final: 0.7872 (m-80) REVERT: N 394 LYS cc_start: 0.9295 (ttmt) cc_final: 0.9050 (ttmm) REVERT: O 136 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8238 (tt) REVERT: O 175 PRO cc_start: 0.9261 (Cg_exo) cc_final: 0.8792 (Cg_endo) REVERT: O 186 THR cc_start: 0.9411 (t) cc_final: 0.9182 (m) REVERT: O 266 GLU cc_start: 0.7816 (pm20) cc_final: 0.7273 (pm20) outliers start: 42 outliers final: 33 residues processed: 323 average time/residue: 0.0941 time to fit residues: 41.5279 Evaluate side-chains 323 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 287 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 425 VAL Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain M residue 425 VAL Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain N residue 411 LEU Chi-restraints excluded: chain O residue 119 ASP Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 158 LYS Chi-restraints excluded: chain O residue 248 SER Chi-restraints excluded: chain O residue 265 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 20 optimal weight: 0.5980 chunk 52 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 43 optimal weight: 0.0010 overall best weight: 2.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.125590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.109523 restraints weight = 14604.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.112663 restraints weight = 7433.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.114829 restraints weight = 4622.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.116338 restraints weight = 3274.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.117434 restraints weight = 2535.669| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9125 Z= 0.146 Angle : 0.642 8.350 12365 Z= 0.324 Chirality : 0.046 0.166 1435 Planarity : 0.006 0.059 1555 Dihedral : 6.325 73.274 1292 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 5.08 % Allowed : 27.62 % Favored : 67.30 % 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: -3.09 (0.23), residues: 1165 helix: -0.89 (0.29), residues: 330 sheet: -2.56 (0.45), residues: 120 loop : -2.67 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 437 TYR 0.018 0.002 TYR I 133 PHE 0.008 0.001 PHE F 208 TRP 0.010 0.001 TRP O 196 HIS 0.007 0.001 HIS F 146 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 9125) covalent geometry : angle 0.64191 (12365) hydrogen bonds : bond 0.03153 ( 235) hydrogen bonds : angle 4.63299 ( 615) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 290 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7541 (mtt180) cc_final: 0.6787 (mpp-170) REVERT: K 394 LYS cc_start: 0.9203 (ttmt) cc_final: 0.8800 (ttmm) REVERT: L 186 THR cc_start: 0.9336 (t) cc_final: 0.9024 (m) REVERT: L 203 TYR cc_start: 0.9161 (t80) cc_final: 0.8753 (t80) REVERT: A 436 MET cc_start: 0.8430 (tmm) cc_final: 0.7927 (tmm) REVERT: B 388 PHE cc_start: 0.8375 (m-10) cc_final: 0.8112 (m-80) REVERT: B 394 LYS cc_start: 0.9268 (ttmt) cc_final: 0.8938 (ttmm) REVERT: C 136 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8605 (tt) REVERT: C 168 ASP cc_start: 0.8858 (t70) cc_final: 0.8280 (t70) REVERT: C 265 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8345 (t) REVERT: E 394 LYS cc_start: 0.9306 (ttmt) cc_final: 0.8947 (ttmm) REVERT: F 168 ASP cc_start: 0.8886 (t70) cc_final: 0.8561 (t0) REVERT: F 265 THR cc_start: 0.8730 (p) cc_final: 0.8269 (t) REVERT: F 266 GLU cc_start: 0.7983 (pm20) cc_final: 0.7735 (pm20) REVERT: G 412 ARG cc_start: 0.7524 (mtt180) cc_final: 0.6904 (mpp-170) REVERT: H 386 TYR cc_start: 0.8840 (t80) cc_final: 0.8312 (t80) REVERT: H 394 LYS cc_start: 0.9263 (ttmt) cc_final: 0.8836 (ttmm) REVERT: I 133 TYR cc_start: 0.8452 (m-80) cc_final: 0.8012 (m-80) REVERT: I 185 TYR cc_start: 0.9205 (p90) cc_final: 0.8851 (p90) REVERT: I 204 SER cc_start: 0.9169 (t) cc_final: 0.8672 (p) REVERT: I 240 ASN cc_start: 0.9051 (t0) cc_final: 0.8785 (t0) REVERT: I 266 GLU cc_start: 0.7723 (pm20) cc_final: 0.7464 (pm20) REVERT: M 412 ARG cc_start: 0.7492 (mtt180) cc_final: 0.6872 (mpp-170) REVERT: M 436 MET cc_start: 0.8237 (tmm) cc_final: 0.7703 (tmm) REVERT: N 394 LYS cc_start: 0.9304 (ttmt) cc_final: 0.9049 (ttmm) REVERT: O 136 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8333 (tt) REVERT: O 175 PRO cc_start: 0.9257 (Cg_exo) cc_final: 0.8801 (Cg_endo) REVERT: O 186 THR cc_start: 0.9458 (t) cc_final: 0.9231 (m) REVERT: O 266 GLU cc_start: 0.7845 (pm20) cc_final: 0.7605 (pm20) outliers start: 48 outliers final: 37 residues processed: 320 average time/residue: 0.0922 time to fit residues: 40.3465 Evaluate side-chains 329 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 289 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 425 VAL Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain G residue 432 THR Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain M residue 425 VAL Chi-restraints excluded: chain M residue 432 THR Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain N residue 411 LEU Chi-restraints excluded: chain O residue 119 ASP Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 158 LYS Chi-restraints excluded: chain O residue 248 SER Chi-restraints excluded: chain O residue 265 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 32 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 22 optimal weight: 8.9990 chunk 26 optimal weight: 0.0050 chunk 67 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.127018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.110827 restraints weight = 14603.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.114034 restraints weight = 7449.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.116217 restraints weight = 4624.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.117756 restraints weight = 3271.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.118863 restraints weight = 2526.779| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9125 Z= 0.126 Angle : 0.622 7.610 12365 Z= 0.314 Chirality : 0.045 0.167 1435 Planarity : 0.006 0.060 1555 Dihedral : 6.308 74.935 1292 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 4.34 % Allowed : 28.47 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.23), residues: 1165 helix: -0.81 (0.29), residues: 340 sheet: -2.60 (0.44), residues: 120 loop : -2.55 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 437 TYR 0.017 0.001 TYR I 133 PHE 0.006 0.001 PHE C 208 TRP 0.010 0.001 TRP O 196 HIS 0.007 0.001 HIS F 146 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9125) covalent geometry : angle 0.62214 (12365) hydrogen bonds : bond 0.02906 ( 235) hydrogen bonds : angle 4.51912 ( 615) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 290 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7522 (mtt180) cc_final: 0.6776 (mpp-170) REVERT: K 394 LYS cc_start: 0.9173 (ttmt) cc_final: 0.8769 (ttmm) REVERT: L 186 THR cc_start: 0.9306 (t) cc_final: 0.9003 (m) REVERT: L 203 TYR cc_start: 0.9153 (t80) cc_final: 0.8758 (t80) REVERT: A 436 MET cc_start: 0.8395 (tmm) cc_final: 0.7895 (tmm) REVERT: B 388 PHE cc_start: 0.8364 (m-10) cc_final: 0.8115 (m-80) REVERT: B 394 LYS cc_start: 0.9222 (ttmt) cc_final: 0.8914 (ttmm) REVERT: C 136 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8558 (tt) REVERT: C 168 ASP cc_start: 0.8849 (t70) cc_final: 0.8280 (t70) REVERT: C 265 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8331 (t) REVERT: E 394 LYS cc_start: 0.9308 (ttmt) cc_final: 0.8962 (ttmm) REVERT: F 168 ASP cc_start: 0.8877 (t70) cc_final: 0.8548 (t0) REVERT: F 265 THR cc_start: 0.8606 (p) cc_final: 0.8285 (t) REVERT: F 266 GLU cc_start: 0.7920 (pm20) cc_final: 0.7680 (pm20) REVERT: G 412 ARG cc_start: 0.7510 (mtt180) cc_final: 0.6890 (mpp-170) REVERT: H 394 LYS cc_start: 0.9285 (ttmt) cc_final: 0.8874 (ttmm) REVERT: I 133 TYR cc_start: 0.8401 (m-80) cc_final: 0.7975 (m-80) REVERT: I 185 TYR cc_start: 0.9204 (p90) cc_final: 0.8854 (p90) REVERT: I 204 SER cc_start: 0.9146 (t) cc_final: 0.8631 (p) REVERT: I 240 ASN cc_start: 0.9042 (t0) cc_final: 0.8773 (t0) REVERT: I 266 GLU cc_start: 0.7754 (pm20) cc_final: 0.7372 (pm20) REVERT: M 412 ARG cc_start: 0.7481 (mtt180) cc_final: 0.6867 (mpp-170) REVERT: M 436 MET cc_start: 0.8251 (tmm) cc_final: 0.7754 (tmm) REVERT: N 388 PHE cc_start: 0.8194 (m-80) cc_final: 0.7920 (m-80) REVERT: N 394 LYS cc_start: 0.9296 (ttmt) cc_final: 0.9031 (ttmm) REVERT: O 136 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8308 (tt) REVERT: O 175 PRO cc_start: 0.9207 (Cg_exo) cc_final: 0.8709 (Cg_endo) REVERT: O 186 THR cc_start: 0.9447 (t) cc_final: 0.9214 (m) REVERT: O 266 GLU cc_start: 0.7864 (pm20) cc_final: 0.7388 (pm20) outliers start: 41 outliers final: 37 residues processed: 315 average time/residue: 0.0945 time to fit residues: 40.9036 Evaluate side-chains 327 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 287 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 425 VAL Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain G residue 432 THR Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain M residue 425 VAL Chi-restraints excluded: chain M residue 432 THR Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain N residue 411 LEU Chi-restraints excluded: chain O residue 119 ASP Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 158 LYS Chi-restraints excluded: chain O residue 248 SER Chi-restraints excluded: chain O residue 265 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 27 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.121398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.105747 restraints weight = 14753.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.108728 restraints weight = 7578.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.110785 restraints weight = 4736.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.112205 restraints weight = 3375.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.113254 restraints weight = 2632.471| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9125 Z= 0.222 Angle : 0.721 9.441 12365 Z= 0.365 Chirality : 0.049 0.174 1435 Planarity : 0.006 0.059 1555 Dihedral : 6.393 69.669 1292 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 4.97 % Allowed : 28.47 % Favored : 66.56 % 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: -3.10 (0.23), residues: 1165 helix: -0.90 (0.29), residues: 330 sheet: -2.61 (0.45), residues: 120 loop : -2.66 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 437 TYR 0.020 0.002 TYR F 161 PHE 0.013 0.002 PHE F 208 TRP 0.019 0.002 TRP C 268 HIS 0.007 0.001 HIS F 146 Details of bonding type rmsd covalent geometry : bond 0.00534 ( 9125) covalent geometry : angle 0.72093 (12365) hydrogen bonds : bond 0.03703 ( 235) hydrogen bonds : angle 4.93451 ( 615) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1561.10 seconds wall clock time: 27 minutes 32.21 seconds (1652.21 seconds total)