Starting phenix.real_space_refine on Sat Jun 7 19:53:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wco_32426/06_2025/7wco_32426.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wco_32426/06_2025/7wco_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wco_32426/06_2025/7wco_32426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wco_32426/06_2025/7wco_32426.map" model { file = "/net/cci-nas-00/data/ceres_data/7wco_32426/06_2025/7wco_32426.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wco_32426/06_2025/7wco_32426.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8950 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 203 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "B" 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: "C" 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: D, G, J, M, F, I, L, O, E, H, K, N Time building chain proxies: 3.98, per 1000 atoms: 0.44 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: 2.11 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.11 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: 1.98 Time building geometry restraints manager: 2.51 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'N' } 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: 2.330 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 21.170 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.980 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.044 0.004 TRP C 196 HIS 0.009 0.002 HIS F 146 PHE 0.012 0.002 PHE C 208 TYR 0.025 0.003 TYR I 161 ARG 0.003 0.001 ARG C 259 Details of bonding type rmsd hydrogen bonds : bond 0.32690 ( 235) hydrogen bonds : angle 11.06485 ( 615) covalent geometry : bond 0.00808 ( 9125) covalent geometry : angle 1.13291 (12365) *********************** 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 : 0.996 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: 0.7635 (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: 0.9734 (t) cc_final: 0.9480 (p) REVERT: D 412 ARG cc_start: 0.7586 (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: 0.9108 (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: 0.2796 time to fit residues: 134.8703 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 : 0.981 ------------------------------------------------------------------------------- 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 92 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3450 r_free = 0.3450 target = 0.128344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.112984 restraints weight = 14806.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.116093 restraints weight = 7634.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.118155 restraints weight = 4778.753| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9125 Z= 0.146 Angle : 0.681 7.826 12365 Z= 0.360 Chirality : 0.046 0.184 1435 Planarity : 0.009 0.067 1555 Dihedral : 7.842 78.853 1294 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 4.87 % Allowed : 15.77 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.78 (0.20), residues: 1165 helix: -3.35 (0.18), residues: 345 sheet: -3.21 (0.42), residues: 120 loop : -3.20 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP O 196 HIS 0.004 0.001 HIS C 193 PHE 0.008 0.001 PHE E 388 TYR 0.020 0.002 TYR I 133 ARG 0.025 0.001 ARG M 437 Details of bonding type rmsd hydrogen bonds : bond 0.04197 ( 235) hydrogen bonds : angle 5.54718 ( 615) covalent geometry : bond 0.00327 ( 9125) covalent geometry : angle 0.68140 (12365) *********************** 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 390 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 344 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7436 (mtt180) cc_final: 0.6688 (mpp-170) REVERT: K 387 MET cc_start: 0.8277 (mtt) cc_final: 0.7982 (mtp) REVERT: K 394 LYS cc_start: 0.9293 (ttmt) cc_final: 0.8810 (ttmm) REVERT: L 112 MET cc_start: 0.7527 (ttm) cc_final: 0.7308 (tpt) REVERT: L 142 MET cc_start: 0.8563 (mtt) cc_final: 0.8357 (mtp) REVERT: L 186 THR cc_start: 0.9087 (t) cc_final: 0.8810 (m) REVERT: L 204 SER cc_start: 0.9279 (t) cc_final: 0.8517 (p) REVERT: L 235 VAL cc_start: 0.9708 (t) cc_final: 0.9491 (p) REVERT: A 412 ARG cc_start: 0.7592 (mtt180) cc_final: 0.6911 (mpp-170) REVERT: B 387 MET cc_start: 0.8216 (mtt) cc_final: 0.7886 (mtp) REVERT: B 394 LYS cc_start: 0.9319 (ttmt) cc_final: 0.8859 (ttmm) REVERT: C 133 TYR cc_start: 0.8794 (m-80) cc_final: 0.8586 (m-80) REVERT: C 135 CYS cc_start: 0.8790 (t) cc_final: 0.8548 (t) REVERT: C 168 ASP cc_start: 0.8840 (t70) cc_final: 0.8299 (t70) REVERT: C 186 THR cc_start: 0.9229 (OUTLIER) cc_final: 0.8911 (m) REVERT: C 265 THR cc_start: 0.8763 (p) cc_final: 0.8255 (t) REVERT: D 412 ARG cc_start: 0.7520 (mtt180) cc_final: 0.6589 (mpp-170) REVERT: E 394 LYS cc_start: 0.9455 (ttmt) cc_final: 0.9018 (ttmm) REVERT: F 111 ARG cc_start: 0.6815 (ptt-90) cc_final: 0.6609 (ptt90) REVERT: F 112 MET cc_start: 0.7514 (ttm) cc_final: 0.7299 (tpp) REVERT: F 153 ASN cc_start: 0.9027 (t0) cc_final: 0.8576 (t0) REVERT: F 156 LEU cc_start: 0.8553 (mp) cc_final: 0.8241 (mt) REVERT: F 204 SER cc_start: 0.9060 (t) cc_final: 0.8319 (p) REVERT: F 240 ASN cc_start: 0.9180 (t0) cc_final: 0.8932 (t0) REVERT: F 265 THR cc_start: 0.8830 (p) cc_final: 0.8574 (t) REVERT: G 412 ARG cc_start: 0.7697 (mtt180) cc_final: 0.6905 (mpp-170) REVERT: H 386 TYR cc_start: 0.8769 (t80) cc_final: 0.8418 (t80) REVERT: H 387 MET cc_start: 0.8340 (mtt) cc_final: 0.8126 (mtp) REVERT: H 394 LYS cc_start: 0.9311 (ttmt) cc_final: 0.8945 (ttmm) REVERT: I 152 ASP cc_start: 0.8219 (t0) cc_final: 0.7959 (t0) REVERT: I 168 ASP cc_start: 0.8921 (t70) cc_final: 0.8665 (t0) REVERT: I 185 TYR cc_start: 0.9186 (p90) cc_final: 0.8969 (p90) REVERT: I 204 SER cc_start: 0.9239 (t) cc_final: 0.8583 (p) REVERT: I 266 GLU cc_start: 0.7807 (pm20) cc_final: 0.7504 (pm20) REVERT: M 412 ARG cc_start: 0.7488 (mtt180) cc_final: 0.6698 (mpp-170) REVERT: N 394 LYS cc_start: 0.9312 (ttmt) cc_final: 0.9025 (ttmm) REVERT: O 204 SER cc_start: 0.9109 (t) cc_final: 0.8495 (p) REVERT: O 240 ASN cc_start: 0.9127 (t0) cc_final: 0.8868 (t0) REVERT: O 266 GLU cc_start: 0.7805 (pm20) cc_final: 0.7532 (pm20) REVERT: O 268 TRP cc_start: 0.8819 (m-10) cc_final: 0.8362 (m-10) outliers start: 46 outliers final: 20 residues processed: 365 average time/residue: 0.2571 time to fit residues: 126.1671 Evaluate side-chains 329 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 308 time to evaluate : 1.274 ------------------------------------------------------------------------------- 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 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 78 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 100 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 96 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.3453 r_free = 0.3453 target = 0.127988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.112523 restraints weight = 14971.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.115667 restraints weight = 7652.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.117794 restraints weight = 4773.082| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9125 Z= 0.133 Angle : 0.644 8.887 12365 Z= 0.329 Chirality : 0.045 0.158 1435 Planarity : 0.007 0.063 1555 Dihedral : 7.006 78.656 1292 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 6.03 % Allowed : 17.57 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.21), residues: 1165 helix: -2.31 (0.23), residues: 345 sheet: -2.89 (0.42), residues: 120 loop : -3.09 (0.20), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP O 196 HIS 0.002 0.001 HIS F 146 PHE 0.006 0.001 PHE I 208 TYR 0.020 0.002 TYR N 386 ARG 0.005 0.000 ARG I 111 Details of bonding type rmsd hydrogen bonds : bond 0.03414 ( 235) hydrogen bonds : angle 5.00621 ( 615) covalent geometry : bond 0.00313 ( 9125) covalent geometry : angle 0.64396 (12365) *********************** 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 372 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 315 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7530 (mtt180) cc_final: 0.6831 (mpp-170) REVERT: K 387 MET cc_start: 0.8228 (mtt) cc_final: 0.7909 (mtp) REVERT: K 394 LYS cc_start: 0.9382 (ttmt) cc_final: 0.8886 (ttmm) REVERT: L 142 MET cc_start: 0.8513 (mtt) cc_final: 0.8266 (mtp) REVERT: L 186 THR cc_start: 0.9158 (t) cc_final: 0.8945 (m) REVERT: B 387 MET cc_start: 0.8187 (mtt) cc_final: 0.7851 (mtp) REVERT: B 394 LYS cc_start: 0.9318 (ttmt) cc_final: 0.8908 (ttmm) REVERT: C 112 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.7114 (tpp) REVERT: C 136 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8575 (tt) REVERT: C 168 ASP cc_start: 0.8820 (t70) cc_final: 0.8157 (t70) REVERT: C 186 THR cc_start: 0.9221 (OUTLIER) cc_final: 0.8934 (m) REVERT: C 265 THR cc_start: 0.8835 (p) cc_final: 0.8272 (t) REVERT: D 412 ARG cc_start: 0.7724 (mtt180) cc_final: 0.6845 (mpp-170) REVERT: E 394 LYS cc_start: 0.9394 (ttmt) cc_final: 0.8934 (ttmm) REVERT: F 156 LEU cc_start: 0.8504 (mp) cc_final: 0.8194 (mp) REVERT: F 168 ASP cc_start: 0.8810 (t70) cc_final: 0.8246 (t70) REVERT: F 189 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8421 (pttm) REVERT: F 204 SER cc_start: 0.8942 (t) cc_final: 0.8267 (p) REVERT: F 240 ASN cc_start: 0.9127 (t0) cc_final: 0.8913 (t0) REVERT: F 265 THR cc_start: 0.8825 (p) cc_final: 0.8326 (t) REVERT: G 412 ARG cc_start: 0.7666 (mtt180) cc_final: 0.7028 (mpp-170) REVERT: H 386 TYR cc_start: 0.8792 (t80) cc_final: 0.8406 (t80) REVERT: H 387 MET cc_start: 0.8352 (mtt) cc_final: 0.8122 (mtp) REVERT: H 394 LYS cc_start: 0.9211 (ttmt) cc_final: 0.8864 (ttmm) REVERT: I 112 MET cc_start: 0.7565 (ttm) cc_final: 0.7350 (tpt) REVERT: I 152 ASP cc_start: 0.8140 (t0) cc_final: 0.7895 (t0) REVERT: I 186 THR cc_start: 0.9367 (t) cc_final: 0.9164 (m) REVERT: I 204 SER cc_start: 0.9316 (t) cc_final: 0.8748 (p) REVERT: I 266 GLU cc_start: 0.7772 (pm20) cc_final: 0.7430 (pm20) REVERT: M 412 ARG cc_start: 0.7445 (mtt180) cc_final: 0.6638 (mpp-170) REVERT: N 388 PHE cc_start: 0.8379 (m-10) cc_final: 0.8159 (m-10) REVERT: N 394 LYS cc_start: 0.9366 (ttmt) cc_final: 0.9066 (ttmm) REVERT: O 136 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8284 (tt) REVERT: O 156 LEU cc_start: 0.8399 (mp) cc_final: 0.7726 (mp) REVERT: O 175 PRO cc_start: 0.9448 (Cg_exo) cc_final: 0.8986 (Cg_endo) REVERT: O 204 SER cc_start: 0.9086 (t) cc_final: 0.8539 (p) REVERT: O 266 GLU cc_start: 0.7787 (pm20) cc_final: 0.7563 (pm20) REVERT: O 268 TRP cc_start: 0.8850 (m-10) cc_final: 0.8567 (m-10) outliers start: 57 outliers final: 38 residues processed: 350 average time/residue: 0.2388 time to fit residues: 110.0686 Evaluate side-chains 345 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 302 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 J residue 437 ARG 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 A residue 425 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 112 MET 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 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 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 425 VAL Chi-restraints excluded: chain G residue 427 VAL Chi-restraints excluded: chain G residue 432 THR 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 427 VAL Chi-restraints excluded: chain M residue 432 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 23 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 108 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.3349 r_free = 0.3349 target = 0.120194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.105197 restraints weight = 15089.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.108100 restraints weight = 7701.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.110083 restraints weight = 4819.473| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9125 Z= 0.256 Angle : 0.748 11.339 12365 Z= 0.383 Chirality : 0.049 0.166 1435 Planarity : 0.007 0.066 1555 Dihedral : 6.893 71.065 1292 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % Rotamer: Outliers : 6.77 % Allowed : 22.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.21), residues: 1165 helix: -1.88 (0.26), residues: 320 sheet: -2.47 (0.38), residues: 170 loop : -3.20 (0.21), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 196 HIS 0.004 0.001 HIS C 193 PHE 0.014 0.002 PHE O 208 TYR 0.024 0.002 TYR F 161 ARG 0.004 0.001 ARG D 438 Details of bonding type rmsd hydrogen bonds : bond 0.04291 ( 235) hydrogen bonds : angle 5.24688 ( 615) covalent geometry : bond 0.00605 ( 9125) covalent geometry : angle 0.74835 (12365) *********************** 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 370 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 306 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7612 (mtt180) cc_final: 0.6941 (mpp-170) REVERT: J 417 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7483 (pp) REVERT: K 387 MET cc_start: 0.8294 (mtt) cc_final: 0.7883 (mtp) REVERT: K 394 LYS cc_start: 0.9379 (ttmt) cc_final: 0.8901 (ttmm) REVERT: L 142 MET cc_start: 0.8546 (mtt) cc_final: 0.8275 (mtp) REVERT: B 387 MET cc_start: 0.8252 (mtt) cc_final: 0.7907 (mtp) REVERT: B 394 LYS cc_start: 0.9369 (ttmt) cc_final: 0.9008 (ttmm) REVERT: C 112 MET cc_start: 0.7420 (OUTLIER) cc_final: 0.7172 (tpp) REVERT: C 136 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8728 (tt) REVERT: C 168 ASP cc_start: 0.8877 (t70) cc_final: 0.8382 (t0) REVERT: C 265 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8299 (t) REVERT: D 412 ARG cc_start: 0.7730 (mtt180) cc_final: 0.6851 (mpp-170) REVERT: E 394 LYS cc_start: 0.9501 (ttmt) cc_final: 0.9120 (ttmm) REVERT: F 168 ASP cc_start: 0.8836 (t70) cc_final: 0.8359 (t0) REVERT: F 189 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.7650 (pmmt) REVERT: F 265 THR cc_start: 0.8961 (p) cc_final: 0.8602 (t) REVERT: F 266 GLU cc_start: 0.8029 (pm20) cc_final: 0.7669 (pm20) REVERT: G 412 ARG cc_start: 0.7680 (mtt180) cc_final: 0.6907 (mpp-170) REVERT: G 417 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7693 (pp) REVERT: H 386 TYR cc_start: 0.8983 (t80) cc_final: 0.8559 (t80) REVERT: H 387 MET cc_start: 0.8446 (mtt) cc_final: 0.8175 (mtp) REVERT: H 394 LYS cc_start: 0.9392 (ttmt) cc_final: 0.8893 (ttmm) REVERT: I 186 THR cc_start: 0.9539 (t) cc_final: 0.9254 (m) REVERT: I 204 SER cc_start: 0.9356 (t) cc_final: 0.8864 (p) REVERT: I 266 GLU cc_start: 0.7884 (pm20) cc_final: 0.7606 (pm20) REVERT: M 412 ARG cc_start: 0.7613 (mtt180) cc_final: 0.7056 (mpp-170) REVERT: M 417 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7732 (pp) REVERT: N 394 LYS cc_start: 0.9379 (ttmt) cc_final: 0.9131 (ttmm) REVERT: O 266 GLU cc_start: 0.7930 (pm20) cc_final: 0.7698 (pm20) outliers start: 64 outliers final: 51 residues processed: 344 average time/residue: 0.2140 time to fit residues: 98.6279 Evaluate side-chains 348 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 290 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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 411 LEU 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 186 THR Chi-restraints excluded: chain L residue 216 LYS Chi-restraints excluded: chain L residue 258 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 116 ILE 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 186 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain F residue 119 ASP 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 411 LEU Chi-restraints excluded: chain I residue 116 ILE 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 417 LEU 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 434 VAL 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 265 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.3342 r_free = 0.3342 target = 0.119346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.104398 restraints weight = 15037.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.107315 restraints weight = 7572.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.109313 restraints weight = 4687.543| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9125 Z= 0.235 Angle : 0.724 11.431 12365 Z= 0.372 Chirality : 0.048 0.197 1435 Planarity : 0.007 0.065 1555 Dihedral : 6.845 70.041 1292 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 8.78 % Allowed : 23.28 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.22), residues: 1165 helix: -1.56 (0.28), residues: 320 sheet: -2.62 (0.47), residues: 120 loop : -3.16 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 196 HIS 0.013 0.001 HIS F 146 PHE 0.014 0.002 PHE O 208 TYR 0.019 0.002 TYR F 161 ARG 0.011 0.001 ARG G 437 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 235) hydrogen bonds : angle 5.16064 ( 615) covalent geometry : bond 0.00563 ( 9125) covalent geometry : angle 0.72369 (12365) *********************** 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 376 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 293 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7604 (mtt180) cc_final: 0.6894 (mpp-170) REVERT: J 417 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7462 (pp) REVERT: K 387 MET cc_start: 0.8331 (mtt) cc_final: 0.7995 (mtp) REVERT: K 394 LYS cc_start: 0.9272 (ttmt) cc_final: 0.8867 (ttmm) REVERT: K 406 VAL cc_start: 0.8373 (p) cc_final: 0.8133 (t) REVERT: B 387 MET cc_start: 0.8198 (mtt) cc_final: 0.7840 (mtp) REVERT: B 394 LYS cc_start: 0.9372 (ttmt) cc_final: 0.9016 (ttmm) REVERT: C 112 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7322 (tpp) REVERT: C 136 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8662 (tt) REVERT: C 168 ASP cc_start: 0.8889 (t70) cc_final: 0.8272 (t70) REVERT: C 265 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8160 (t) REVERT: D 412 ARG cc_start: 0.7727 (mtt180) cc_final: 0.6842 (mpp-170) REVERT: E 394 LYS cc_start: 0.9430 (ttmt) cc_final: 0.9106 (ttmm) REVERT: F 189 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.7650 (pmmt) REVERT: F 266 GLU cc_start: 0.8025 (pm20) cc_final: 0.7773 (pm20) REVERT: G 412 ARG cc_start: 0.7593 (mtt180) cc_final: 0.6844 (mpp-170) REVERT: G 417 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7703 (pp) REVERT: G 436 MET cc_start: 0.8760 (ptm) cc_final: 0.8497 (tmm) REVERT: H 386 TYR cc_start: 0.8976 (t80) cc_final: 0.8571 (t80) REVERT: H 387 MET cc_start: 0.8413 (mtt) cc_final: 0.8165 (mtp) REVERT: H 394 LYS cc_start: 0.9361 (ttmt) cc_final: 0.8841 (ttmm) REVERT: I 204 SER cc_start: 0.9332 (t) cc_final: 0.8826 (p) REVERT: I 266 GLU cc_start: 0.7864 (pm20) cc_final: 0.7400 (pm20) REVERT: M 412 ARG cc_start: 0.7614 (mtt180) cc_final: 0.7041 (mpp-170) REVERT: M 417 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7803 (pp) REVERT: N 386 TYR cc_start: 0.8979 (t80) cc_final: 0.8507 (t80) REVERT: N 394 LYS cc_start: 0.9357 (ttmt) cc_final: 0.9092 (ttmm) REVERT: N 406 VAL cc_start: 0.8464 (t) cc_final: 0.8175 (p) REVERT: O 114 MET cc_start: 0.7353 (pmt) cc_final: 0.6977 (pmt) REVERT: O 266 GLU cc_start: 0.7943 (pm20) cc_final: 0.7682 (pm20) outliers start: 83 outliers final: 62 residues processed: 339 average time/residue: 0.2304 time to fit residues: 104.7272 Evaluate side-chains 353 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 284 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 402 THR Chi-restraints excluded: chain L residue 114 MET 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 L residue 165 SER Chi-restraints excluded: chain L residue 186 THR 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 434 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 112 MET 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 147 VAL 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 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 D residue 436 MET Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain F residue 116 ILE 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 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 F residue 258 THR 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 377 VAL Chi-restraints excluded: chain H residue 411 LEU 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 417 LEU 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 434 VAL Chi-restraints excluded: chain M residue 436 MET Chi-restraints excluded: chain N residue 377 VAL 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 147 VAL Chi-restraints excluded: chain O residue 158 LYS 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 85 optimal weight: 9.9990 chunk 105 optimal weight: 0.0370 chunk 71 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 28 optimal weight: 0.0370 chunk 27 optimal weight: 0.7980 chunk 82 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- 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 = 0.3459 r_free = 0.3459 target = 0.128130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.112307 restraints weight = 14489.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.115525 restraints weight = 7324.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.117732 restraints weight = 4506.838| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9125 Z= 0.111 Angle : 0.610 7.376 12365 Z= 0.309 Chirality : 0.045 0.176 1435 Planarity : 0.007 0.063 1555 Dihedral : 6.650 78.225 1292 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 4.23 % Allowed : 28.04 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.24), residues: 1165 helix: -0.72 (0.29), residues: 325 sheet: -2.49 (0.47), residues: 120 loop : -2.52 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 268 HIS 0.009 0.001 HIS F 146 PHE 0.009 0.001 PHE E 388 TYR 0.014 0.001 TYR O 203 ARG 0.014 0.000 ARG J 437 Details of bonding type rmsd hydrogen bonds : bond 0.02937 ( 235) hydrogen bonds : angle 4.66896 ( 615) covalent geometry : bond 0.00252 ( 9125) covalent geometry : angle 0.60998 (12365) *********************** 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 355 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 315 time to evaluate : 1.068 Fit side-chains revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7545 (mtt180) cc_final: 0.6811 (mpp-170) REVERT: K 394 LYS cc_start: 0.9203 (ttmt) cc_final: 0.8859 (ttmm) REVERT: L 186 THR cc_start: 0.9225 (t) cc_final: 0.8967 (m) REVERT: B 387 MET cc_start: 0.8013 (mtt) cc_final: 0.7808 (mtp) REVERT: B 388 PHE cc_start: 0.8432 (m-10) cc_final: 0.8161 (m-80) REVERT: B 394 LYS cc_start: 0.9313 (ttmt) cc_final: 0.8966 (ttmm) REVERT: C 136 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8327 (tt) REVERT: C 168 ASP cc_start: 0.8833 (t70) cc_final: 0.8269 (t70) REVERT: C 195 ASN cc_start: 0.9008 (p0) cc_final: 0.8785 (p0) REVERT: C 265 THR cc_start: 0.8750 (p) cc_final: 0.8283 (t) REVERT: E 388 PHE cc_start: 0.8171 (m-10) cc_final: 0.7938 (m-10) REVERT: E 394 LYS cc_start: 0.9326 (ttmt) cc_final: 0.9027 (ttmm) REVERT: F 189 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8476 (pttm) REVERT: F 265 THR cc_start: 0.8756 (p) cc_final: 0.8303 (t) REVERT: G 412 ARG cc_start: 0.7460 (mtt180) cc_final: 0.6861 (mpp-170) REVERT: H 386 TYR cc_start: 0.8798 (t80) cc_final: 0.8401 (t80) REVERT: H 394 LYS cc_start: 0.9275 (ttmt) cc_final: 0.8893 (ttmm) REVERT: I 175 PRO cc_start: 0.9532 (Cg_exo) cc_final: 0.9285 (Cg_endo) REVERT: I 204 SER cc_start: 0.9250 (t) cc_final: 0.8816 (p) REVERT: I 266 GLU cc_start: 0.7764 (pm20) cc_final: 0.7424 (pm20) REVERT: M 412 ARG cc_start: 0.7557 (mtt180) cc_final: 0.6866 (mpp-170) REVERT: N 394 LYS cc_start: 0.9268 (ttmt) cc_final: 0.9037 (ttmm) REVERT: O 136 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8062 (tt) REVERT: O 175 PRO cc_start: 0.9166 (Cg_exo) cc_final: 0.8642 (Cg_endo) REVERT: O 186 THR cc_start: 0.9366 (t) cc_final: 0.9143 (m) REVERT: O 204 SER cc_start: 0.9134 (t) cc_final: 0.8533 (p) REVERT: O 266 GLU cc_start: 0.7872 (pm20) cc_final: 0.7351 (pm20) outliers start: 40 outliers final: 23 residues processed: 338 average time/residue: 0.2175 time to fit residues: 99.0105 Evaluate side-chains 311 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 285 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 415 CYS 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 D residue 417 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 165 SER Chi-restraints excluded: chain F residue 189 LYS Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 158 LYS 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 Chi-restraints excluded: chain O residue 174 ILE 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 67 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 62 optimal weight: 0.4980 chunk 50 optimal weight: 0.0870 chunk 106 optimal weight: 9.9990 chunk 48 optimal weight: 0.0970 overall best weight: 2.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.125853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.109836 restraints weight = 14741.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.112966 restraints weight = 7452.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.115149 restraints weight = 4599.756| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.4212 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= 0.136 Angle : 0.660 10.856 12365 Z= 0.327 Chirality : 0.046 0.172 1435 Planarity : 0.007 0.063 1555 Dihedral : 6.449 76.083 1292 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 4.13 % Allowed : 28.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.23), residues: 1165 helix: -1.13 (0.28), residues: 340 sheet: -2.55 (0.46), residues: 120 loop : -2.69 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 268 HIS 0.007 0.001 HIS F 146 PHE 0.007 0.001 PHE O 208 TYR 0.015 0.001 TYR F 161 ARG 0.009 0.001 ARG A 437 Details of bonding type rmsd hydrogen bonds : bond 0.03296 ( 235) hydrogen bonds : angle 4.75385 ( 615) covalent geometry : bond 0.00326 ( 9125) covalent geometry : angle 0.66009 (12365) *********************** 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 332 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 293 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7547 (mtt180) cc_final: 0.6802 (mpp-170) REVERT: K 394 LYS cc_start: 0.9265 (ttmt) cc_final: 0.8918 (ttmm) REVERT: L 186 THR cc_start: 0.9284 (t) cc_final: 0.9000 (m) REVERT: A 436 MET cc_start: 0.8239 (tmm) cc_final: 0.7754 (tmm) REVERT: B 387 MET cc_start: 0.8000 (mtt) cc_final: 0.7699 (mtp) REVERT: B 388 PHE cc_start: 0.8447 (m-10) cc_final: 0.8187 (m-80) REVERT: B 394 LYS cc_start: 0.9317 (ttmt) cc_final: 0.8972 (ttmm) REVERT: C 136 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8567 (tt) REVERT: C 168 ASP cc_start: 0.8873 (t70) cc_final: 0.8300 (t70) REVERT: C 265 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8319 (t) REVERT: E 394 LYS cc_start: 0.9382 (ttmt) cc_final: 0.9066 (ttmm) REVERT: F 189 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8432 (pttm) REVERT: F 265 THR cc_start: 0.8770 (p) cc_final: 0.8319 (t) REVERT: F 266 GLU cc_start: 0.7886 (pm20) cc_final: 0.7647 (pm20) REVERT: G 412 ARG cc_start: 0.7551 (mtt180) cc_final: 0.6793 (mpp-170) REVERT: H 394 LYS cc_start: 0.9272 (ttmt) cc_final: 0.8846 (ttmm) REVERT: H 411 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7461 (tp) REVERT: I 204 SER cc_start: 0.9214 (t) cc_final: 0.8690 (p) REVERT: I 266 GLU cc_start: 0.7805 (pm20) cc_final: 0.7495 (pm20) REVERT: M 412 ARG cc_start: 0.7575 (mtt180) cc_final: 0.6874 (mpp-170) REVERT: N 394 LYS cc_start: 0.9327 (ttmt) cc_final: 0.9086 (ttmm) REVERT: O 114 MET cc_start: 0.7344 (pmt) cc_final: 0.7026 (pmt) REVERT: O 186 THR cc_start: 0.9379 (t) cc_final: 0.9134 (m) REVERT: O 204 SER cc_start: 0.9191 (t) cc_final: 0.8605 (p) REVERT: O 266 GLU cc_start: 0.7873 (pm20) cc_final: 0.7623 (pm20) outliers start: 39 outliers final: 26 residues processed: 314 average time/residue: 0.2262 time to fit residues: 95.4194 Evaluate side-chains 317 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 287 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 189 LYS Chi-restraints excluded: chain F residue 193 HIS 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 436 MET 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 265 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 32 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 107 optimal weight: 0.0470 chunk 98 optimal weight: 0.0670 chunk 76 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 52 optimal weight: 10.0000 overall best weight: 1.3820 ------------------------------------------------------------------------------- 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 = 0.3442 r_free = 0.3442 target = 0.127298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.111121 restraints weight = 14765.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.114345 restraints weight = 7384.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.116594 restraints weight = 4503.736| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9125 Z= 0.119 Angle : 0.639 9.770 12365 Z= 0.319 Chirality : 0.045 0.165 1435 Planarity : 0.006 0.062 1555 Dihedral : 6.440 79.001 1292 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 4.13 % Allowed : 28.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.23), residues: 1165 helix: -0.99 (0.27), residues: 360 sheet: -2.53 (0.46), residues: 120 loop : -2.61 (0.21), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 196 HIS 0.007 0.001 HIS F 146 PHE 0.007 0.001 PHE E 388 TYR 0.023 0.001 TYR I 133 ARG 0.007 0.000 ARG G 437 Details of bonding type rmsd hydrogen bonds : bond 0.02975 ( 235) hydrogen bonds : angle 4.60865 ( 615) covalent geometry : bond 0.00286 ( 9125) covalent geometry : angle 0.63916 (12365) *********************** 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 332 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 293 time to evaluate : 1.381 Fit side-chains revert: symmetry clash REVERT: K 394 LYS cc_start: 0.9231 (ttmt) cc_final: 0.8864 (ttmm) REVERT: L 186 THR cc_start: 0.9264 (t) cc_final: 0.8973 (m) REVERT: A 436 MET cc_start: 0.8240 (tmm) cc_final: 0.7911 (tmm) REVERT: B 388 PHE cc_start: 0.8440 (m-10) cc_final: 0.8158 (m-80) REVERT: B 394 LYS cc_start: 0.9282 (ttmt) cc_final: 0.8942 (ttmm) REVERT: C 136 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8533 (tt) REVERT: C 168 ASP cc_start: 0.8847 (t70) cc_final: 0.8293 (t70) REVERT: C 265 THR cc_start: 0.8723 (OUTLIER) cc_final: 0.8317 (t) REVERT: E 394 LYS cc_start: 0.9360 (ttmt) cc_final: 0.9048 (ttmm) REVERT: F 168 ASP cc_start: 0.8875 (t70) cc_final: 0.8439 (t0) REVERT: F 189 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8444 (pttm) REVERT: F 265 THR cc_start: 0.8613 (p) cc_final: 0.8242 (t) REVERT: F 266 GLU cc_start: 0.7891 (pm20) cc_final: 0.7630 (pm20) REVERT: G 412 ARG cc_start: 0.7541 (mtt180) cc_final: 0.6958 (mpp-170) REVERT: H 394 LYS cc_start: 0.9199 (ttmt) cc_final: 0.8895 (ttmm) REVERT: I 112 MET cc_start: 0.7487 (tpt) cc_final: 0.7070 (tpp) REVERT: I 123 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7718 (mt-10) REVERT: I 185 TYR cc_start: 0.9175 (p90) cc_final: 0.8746 (p90) REVERT: I 204 SER cc_start: 0.9124 (t) cc_final: 0.8588 (p) REVERT: I 266 GLU cc_start: 0.7775 (pm20) cc_final: 0.7478 (pm20) REVERT: M 412 ARG cc_start: 0.7577 (mtt180) cc_final: 0.6859 (mpp-170) REVERT: N 388 PHE cc_start: 0.8202 (m-80) cc_final: 0.7912 (m-80) REVERT: N 394 LYS cc_start: 0.9265 (ttmt) cc_final: 0.9013 (ttmm) REVERT: O 114 MET cc_start: 0.7233 (pmt) cc_final: 0.6905 (pmt) REVERT: O 175 PRO cc_start: 0.9132 (Cg_exo) cc_final: 0.8603 (Cg_endo) REVERT: O 186 THR cc_start: 0.9367 (t) cc_final: 0.9120 (m) REVERT: O 204 SER cc_start: 0.9318 (t) cc_final: 0.8852 (p) REVERT: O 266 GLU cc_start: 0.7826 (pm20) cc_final: 0.7585 (pm20) outliers start: 39 outliers final: 31 residues processed: 315 average time/residue: 0.2555 time to fit residues: 108.3219 Evaluate side-chains 316 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 282 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 397 THR 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 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 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 397 THR 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 189 LYS Chi-restraints excluded: chain F residue 193 HIS 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 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 265 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 94 optimal weight: 0.0470 chunk 36 optimal weight: 8.9990 chunk 48 optimal weight: 0.0270 chunk 15 optimal weight: 2.9990 chunk 39 optimal weight: 0.0020 chunk 55 optimal weight: 9.9990 chunk 90 optimal weight: 0.2980 chunk 54 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 overall best weight: 0.2344 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.133348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.116982 restraints weight = 14381.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.120339 restraints weight = 7367.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.122661 restraints weight = 4540.744| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4795 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 : 0.607 7.826 12365 Z= 0.304 Chirality : 0.044 0.161 1435 Planarity : 0.006 0.061 1555 Dihedral : 6.308 82.899 1292 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 3.39 % Allowed : 29.63 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.23), residues: 1165 helix: -0.76 (0.28), residues: 360 sheet: -2.54 (0.44), residues: 120 loop : -2.48 (0.21), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 196 HIS 0.006 0.001 HIS F 146 PHE 0.004 0.001 PHE E 388 TYR 0.013 0.001 TYR O 203 ARG 0.006 0.000 ARG G 437 Details of bonding type rmsd hydrogen bonds : bond 0.02444 ( 235) hydrogen bonds : angle 4.50703 ( 615) covalent geometry : bond 0.00260 ( 9125) covalent geometry : angle 0.60680 (12365) *********************** 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 324 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 292 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 394 LYS cc_start: 0.9099 (ttmt) cc_final: 0.8807 (ttmm) REVERT: L 112 MET cc_start: 0.7651 (tpt) cc_final: 0.7230 (tpp) REVERT: L 186 THR cc_start: 0.9210 (t) cc_final: 0.8915 (m) REVERT: A 436 MET cc_start: 0.7923 (tmm) cc_final: 0.7596 (tmm) REVERT: B 388 PHE cc_start: 0.8316 (m-10) cc_final: 0.8009 (m-80) REVERT: B 394 LYS cc_start: 0.9283 (ttmt) cc_final: 0.8955 (ttmm) REVERT: C 168 ASP cc_start: 0.8796 (t70) cc_final: 0.8301 (t70) REVERT: E 394 LYS cc_start: 0.9341 (ttmt) cc_final: 0.9025 (ttmm) REVERT: F 168 ASP cc_start: 0.8815 (t70) cc_final: 0.8362 (t0) REVERT: F 186 THR cc_start: 0.9213 (t) cc_final: 0.8931 (m) REVERT: F 189 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8602 (pttm) REVERT: F 265 THR cc_start: 0.8401 (p) cc_final: 0.8160 (t) REVERT: H 394 LYS cc_start: 0.9240 (ttmt) cc_final: 0.8989 (ttmm) REVERT: I 112 MET cc_start: 0.7272 (tpt) cc_final: 0.6904 (tpp) REVERT: I 185 TYR cc_start: 0.9149 (p90) cc_final: 0.8773 (p90) REVERT: I 266 GLU cc_start: 0.7741 (pm20) cc_final: 0.7460 (pm20) REVERT: M 412 ARG cc_start: 0.7450 (mtt180) cc_final: 0.6640 (mpp-170) REVERT: M 436 MET cc_start: 0.7922 (tmm) cc_final: 0.7603 (tmm) REVERT: N 388 PHE cc_start: 0.8191 (m-80) cc_final: 0.7913 (m-80) REVERT: N 394 LYS cc_start: 0.9246 (ttmt) cc_final: 0.9040 (ttmm) REVERT: O 175 PRO cc_start: 0.9173 (Cg_exo) cc_final: 0.8645 (Cg_endo) REVERT: O 186 THR cc_start: 0.9303 (t) cc_final: 0.9045 (m) REVERT: O 204 SER cc_start: 0.9225 (t) cc_final: 0.8776 (p) REVERT: O 266 GLU cc_start: 0.7794 (pm20) cc_final: 0.7565 (pm20) outliers start: 32 outliers final: 24 residues processed: 312 average time/residue: 0.2172 time to fit residues: 91.5287 Evaluate side-chains 309 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 284 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 265 THR Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 189 LYS 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 N residue 397 THR 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 265 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 95 optimal weight: 20.0000 chunk 72 optimal weight: 0.4980 chunk 97 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 109 optimal weight: 0.0470 chunk 69 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.4882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 202 GLN I 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.130347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.114140 restraints weight = 14382.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.117363 restraints weight = 7332.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.119621 restraints weight = 4520.141| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9125 Z= 0.121 Angle : 0.644 10.155 12365 Z= 0.317 Chirality : 0.045 0.164 1435 Planarity : 0.006 0.060 1555 Dihedral : 6.152 78.979 1292 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 2.96 % Allowed : 28.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.23), residues: 1165 helix: -0.45 (0.29), residues: 340 sheet: -2.59 (0.44), residues: 120 loop : -2.32 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 268 HIS 0.006 0.001 HIS L 146 PHE 0.008 0.001 PHE E 388 TYR 0.014 0.001 TYR C 161 ARG 0.009 0.000 ARG M 437 Details of bonding type rmsd hydrogen bonds : bond 0.02705 ( 235) hydrogen bonds : angle 4.48463 ( 615) covalent geometry : bond 0.00292 ( 9125) covalent geometry : angle 0.64443 (12365) ********************** 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 315 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 287 time to evaluate : 1.058 Fit side-chains REVERT: K 394 LYS cc_start: 0.9144 (ttmt) cc_final: 0.8857 (ttmm) REVERT: L 112 MET cc_start: 0.7679 (tpt) cc_final: 0.7224 (tpp) REVERT: L 186 THR cc_start: 0.9225 (t) cc_final: 0.8929 (m) REVERT: A 436 MET cc_start: 0.7903 (tmm) cc_final: 0.7594 (tmm) REVERT: B 388 PHE cc_start: 0.8324 (m-10) cc_final: 0.8052 (m-80) REVERT: B 394 LYS cc_start: 0.9277 (ttmt) cc_final: 0.8926 (ttmm) REVERT: C 168 ASP cc_start: 0.8811 (t70) cc_final: 0.8332 (t70) REVERT: E 394 LYS cc_start: 0.9343 (ttmt) cc_final: 0.9022 (ttmm) REVERT: F 168 ASP cc_start: 0.8810 (t70) cc_final: 0.8506 (t0) REVERT: F 186 THR cc_start: 0.9257 (t) cc_final: 0.8998 (m) REVERT: F 265 THR cc_start: 0.8422 (p) cc_final: 0.8182 (t) REVERT: H 394 LYS cc_start: 0.9254 (ttmt) cc_final: 0.9000 (ttmm) REVERT: I 112 MET cc_start: 0.7274 (tpt) cc_final: 0.6993 (tpp) REVERT: I 185 TYR cc_start: 0.9166 (p90) cc_final: 0.8809 (p90) REVERT: I 236 LEU cc_start: 0.9268 (pt) cc_final: 0.9003 (pp) REVERT: I 266 GLU cc_start: 0.7711 (pm20) cc_final: 0.7477 (pm20) REVERT: M 412 ARG cc_start: 0.7580 (mtt180) cc_final: 0.6892 (mpp-170) REVERT: M 436 MET cc_start: 0.7687 (tmm) cc_final: 0.7466 (tmm) REVERT: N 394 LYS cc_start: 0.9284 (ttmt) cc_final: 0.9072 (ttmm) REVERT: O 186 THR cc_start: 0.9356 (t) cc_final: 0.9113 (m) REVERT: O 204 SER cc_start: 0.9261 (t) cc_final: 0.8800 (p) REVERT: O 266 GLU cc_start: 0.7809 (pm20) cc_final: 0.7602 (pm20) outliers start: 28 outliers final: 27 residues processed: 303 average time/residue: 0.2184 time to fit residues: 89.3247 Evaluate side-chains 309 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 282 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 406 VAL 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 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 265 THR Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain E residue 397 THR 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 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 N residue 397 THR 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 265 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3401 r_free = 0.3401 target = 0.124805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.108774 restraints weight = 14778.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.111888 restraints weight = 7533.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.114023 restraints weight = 4681.495| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9125 Z= 0.189 Angle : 0.728 10.382 12365 Z= 0.362 Chirality : 0.048 0.173 1435 Planarity : 0.007 0.072 1555 Dihedral : 6.276 72.542 1292 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 3.49 % Allowed : 29.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.23), residues: 1165 helix: -0.56 (0.29), residues: 330 sheet: -2.11 (0.39), residues: 170 loop : -2.45 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 268 HIS 0.007 0.001 HIS L 146 PHE 0.010 0.001 PHE F 208 TYR 0.015 0.002 TYR C 161 ARG 0.010 0.001 ARG J 437 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 235) hydrogen bonds : angle 4.91133 ( 615) covalent geometry : bond 0.00458 ( 9125) covalent geometry : angle 0.72771 (12365) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3330.86 seconds wall clock time: 59 minutes 15.20 seconds (3555.20 seconds total)