Starting phenix.real_space_refine on Sat Dec 28 18:53:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wco_32426/12_2024/7wco_32426.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wco_32426/12_2024/7wco_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_32426/12_2024/7wco_32426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wco_32426/12_2024/7wco_32426.map" model { file = "/net/cci-nas-00/data/ceres_data/7wco_32426/12_2024/7wco_32426.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wco_32426/12_2024/7wco_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-5532/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: 3.83, per 1000 atoms: 0.43 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: 2.05 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: 1.01 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: 2.07 Time building geometry restraints manager: 2.39 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.140 Find NCS groups from input model: 0.280 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: 25.520 ------------------------------------------------------------------------------- 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= 0.544 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 *********************** 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: 0.2323 time to fit residues: 111.2719 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 : 1.034 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 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= 0.217 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 *********************** 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 : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7427 (mtt180) cc_final: 0.6652 (mpp-170) REVERT: K 387 MET cc_start: 0.8288 (mtt) cc_final: 0.7991 (mtp) REVERT: K 394 LYS cc_start: 0.9315 (ttmt) cc_final: 0.8841 (ttmm) REVERT: L 112 MET cc_start: 0.7664 (ttm) cc_final: 0.7351 (tpt) REVERT: L 142 MET cc_start: 0.8601 (mtt) cc_final: 0.8378 (mtp) REVERT: L 186 THR cc_start: 0.9101 (t) cc_final: 0.8822 (m) REVERT: L 204 SER cc_start: 0.9275 (t) cc_final: 0.8513 (p) REVERT: L 207 ARG cc_start: 0.8795 (ptm160) cc_final: 0.8581 (mtp-110) REVERT: L 235 VAL cc_start: 0.9709 (t) cc_final: 0.9476 (p) REVERT: A 412 ARG cc_start: 0.7594 (mtt180) cc_final: 0.6879 (mpp-170) REVERT: B 387 MET cc_start: 0.8205 (mtt) cc_final: 0.7876 (mtp) REVERT: B 394 LYS cc_start: 0.9323 (ttmt) cc_final: 0.8865 (ttmm) REVERT: C 133 TYR cc_start: 0.8830 (m-80) cc_final: 0.8615 (m-80) REVERT: C 135 CYS cc_start: 0.8802 (t) cc_final: 0.8558 (t) REVERT: C 168 ASP cc_start: 0.8843 (t70) cc_final: 0.8279 (t70) REVERT: C 186 THR cc_start: 0.9233 (OUTLIER) cc_final: 0.8914 (m) REVERT: C 265 THR cc_start: 0.8800 (p) cc_final: 0.8277 (t) REVERT: D 412 ARG cc_start: 0.7520 (mtt180) cc_final: 0.6572 (mpp-170) REVERT: E 394 LYS cc_start: 0.9457 (ttmt) cc_final: 0.9019 (ttmm) REVERT: F 111 ARG cc_start: 0.6758 (ptt-90) cc_final: 0.6549 (ptt90) REVERT: F 112 MET cc_start: 0.7681 (ttm) cc_final: 0.7388 (tpp) REVERT: F 153 ASN cc_start: 0.9076 (t0) cc_final: 0.8596 (t0) REVERT: F 156 LEU cc_start: 0.8446 (mp) cc_final: 0.8123 (mt) REVERT: F 204 SER cc_start: 0.9065 (t) cc_final: 0.8324 (p) REVERT: F 240 ASN cc_start: 0.9239 (t0) cc_final: 0.9001 (t0) REVERT: F 265 THR cc_start: 0.8884 (p) cc_final: 0.8600 (t) REVERT: G 412 ARG cc_start: 0.7696 (mtt180) cc_final: 0.6877 (mpp-170) REVERT: H 386 TYR cc_start: 0.8777 (t80) cc_final: 0.8422 (t80) REVERT: H 387 MET cc_start: 0.8355 (mtt) cc_final: 0.8130 (mtp) REVERT: H 394 LYS cc_start: 0.9324 (ttmt) cc_final: 0.8961 (ttmm) REVERT: I 152 ASP cc_start: 0.8286 (t0) cc_final: 0.8023 (t0) REVERT: I 168 ASP cc_start: 0.8940 (t70) cc_final: 0.8666 (t0) REVERT: I 185 TYR cc_start: 0.9202 (p90) cc_final: 0.8977 (p90) REVERT: I 204 SER cc_start: 0.9236 (t) cc_final: 0.8578 (p) REVERT: I 266 GLU cc_start: 0.7817 (pm20) cc_final: 0.7500 (pm20) REVERT: M 412 ARG cc_start: 0.7481 (mtt180) cc_final: 0.6667 (mpp-170) REVERT: N 394 LYS cc_start: 0.9324 (ttmt) cc_final: 0.9038 (ttmm) REVERT: O 112 MET cc_start: 0.7388 (ttm) cc_final: 0.7063 (mmm) REVERT: O 204 SER cc_start: 0.9113 (t) cc_final: 0.8507 (p) REVERT: O 240 ASN cc_start: 0.9177 (t0) cc_final: 0.8928 (t0) REVERT: O 266 GLU cc_start: 0.7812 (pm20) cc_final: 0.7522 (pm20) REVERT: O 268 TRP cc_start: 0.8820 (m-10) cc_final: 0.8370 (m-10) outliers start: 46 outliers final: 20 residues processed: 365 average time/residue: 0.2254 time to fit residues: 109.4826 Evaluate side-chains 330 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 309 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 55 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3198 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= 0.302 Angle : 0.689 10.171 12365 Z= 0.357 Chirality : 0.047 0.166 1435 Planarity : 0.008 0.065 1555 Dihedral : 7.009 74.081 1292 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 6.56 % Allowed : 17.67 % Favored : 75.77 % 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: -4.21 (0.21), residues: 1165 helix: -2.33 (0.24), residues: 320 sheet: -2.60 (0.37), residues: 170 loop : -3.22 (0.20), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP O 196 HIS 0.003 0.001 HIS C 193 PHE 0.010 0.002 PHE I 208 TYR 0.021 0.002 TYR F 161 ARG 0.005 0.001 ARG I 111 *********************** 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 370 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 308 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7521 (mtt180) cc_final: 0.6736 (mpp-170) REVERT: K 387 MET cc_start: 0.8404 (mtt) cc_final: 0.8021 (mtp) REVERT: K 394 LYS cc_start: 0.9423 (ttmt) cc_final: 0.8956 (ttmm) REVERT: L 112 MET cc_start: 0.7587 (ttm) cc_final: 0.7340 (tpt) REVERT: L 142 MET cc_start: 0.8584 (mtt) cc_final: 0.8303 (mtp) REVERT: L 168 ASP cc_start: 0.8840 (t0) cc_final: 0.8515 (t0) REVERT: L 186 THR cc_start: 0.9222 (OUTLIER) cc_final: 0.9000 (m) REVERT: L 207 ARG cc_start: 0.8901 (ptm160) cc_final: 0.8658 (ptm160) REVERT: L 222 ARG cc_start: 0.8863 (mmt180) cc_final: 0.8480 (mmm160) REVERT: L 235 VAL cc_start: 0.9702 (t) cc_final: 0.9489 (p) REVERT: B 387 MET cc_start: 0.8229 (mtt) cc_final: 0.7854 (mtp) REVERT: B 394 LYS cc_start: 0.9395 (ttmt) cc_final: 0.9043 (ttmm) REVERT: C 112 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7341 (tpp) REVERT: C 133 TYR cc_start: 0.8959 (m-80) cc_final: 0.8732 (m-80) REVERT: C 135 CYS cc_start: 0.8896 (t) cc_final: 0.8638 (t) REVERT: C 136 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8614 (tt) REVERT: C 168 ASP cc_start: 0.8873 (t70) cc_final: 0.8191 (t0) REVERT: C 189 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8823 (pttm) REVERT: C 265 THR cc_start: 0.8893 (p) cc_final: 0.8296 (t) REVERT: D 412 ARG cc_start: 0.7580 (mtt180) cc_final: 0.6627 (mpp-170) REVERT: E 388 PHE cc_start: 0.8241 (m-10) cc_final: 0.8025 (m-10) REVERT: E 394 LYS cc_start: 0.9499 (ttmt) cc_final: 0.9076 (ttmm) REVERT: F 153 ASN cc_start: 0.9236 (t0) cc_final: 0.8949 (t0) REVERT: F 156 LEU cc_start: 0.8513 (mp) cc_final: 0.8090 (mt) REVERT: F 189 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.7726 (pmmt) REVERT: F 240 ASN cc_start: 0.9200 (t0) cc_final: 0.8991 (t0) REVERT: F 265 THR cc_start: 0.8956 (p) cc_final: 0.8635 (t) REVERT: G 412 ARG cc_start: 0.7648 (mtt180) cc_final: 0.6833 (mpp-170) REVERT: H 386 TYR cc_start: 0.8879 (t80) cc_final: 0.8479 (t80) REVERT: H 387 MET cc_start: 0.8443 (mtt) cc_final: 0.8223 (mtp) REVERT: H 394 LYS cc_start: 0.9423 (ttmt) cc_final: 0.8935 (ttmm) REVERT: I 112 MET cc_start: 0.7873 (ttm) cc_final: 0.7423 (tpt) REVERT: I 204 SER cc_start: 0.9343 (t) cc_final: 0.8824 (p) REVERT: I 266 GLU cc_start: 0.7834 (pm20) cc_final: 0.7474 (pm20) REVERT: M 412 ARG cc_start: 0.7628 (mtt180) cc_final: 0.6920 (mpp-170) REVERT: N 394 LYS cc_start: 0.9399 (ttmt) cc_final: 0.9142 (ttmm) REVERT: O 112 MET cc_start: 0.7276 (ttm) cc_final: 0.7067 (mmm) REVERT: O 175 PRO cc_start: 0.9489 (Cg_exo) cc_final: 0.9288 (Cg_endo) REVERT: O 204 SER cc_start: 0.9231 (t) cc_final: 0.8669 (p) REVERT: O 266 GLU cc_start: 0.7913 (pm20) cc_final: 0.7672 (pm20) outliers start: 62 outliers final: 43 residues processed: 344 average time/residue: 0.2343 time to fit residues: 106.4740 Evaluate side-chains 346 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 298 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 377 VAL Chi-restraints excluded: chain K residue 411 LEU 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 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 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 189 LYS 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 E residue 377 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 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 434 VAL 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 98 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9125 Z= 0.295 Angle : 0.679 10.202 12365 Z= 0.348 Chirality : 0.047 0.181 1435 Planarity : 0.007 0.065 1555 Dihedral : 6.824 73.223 1292 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 6.98 % Allowed : 22.43 % Favored : 70.58 % 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: -3.83 (0.22), residues: 1165 helix: -1.65 (0.27), residues: 320 sheet: -2.57 (0.47), residues: 120 loop : -3.14 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 196 HIS 0.014 0.001 HIS L 146 PHE 0.010 0.002 PHE O 208 TYR 0.018 0.002 TYR F 161 ARG 0.007 0.001 ARG G 437 *********************** 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 374 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 308 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7570 (mtt180) cc_final: 0.6784 (mpp-170) REVERT: J 417 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7265 (pp) REVERT: K 387 MET cc_start: 0.8313 (mtt) cc_final: 0.7904 (mtp) REVERT: K 394 LYS cc_start: 0.9384 (ttmt) cc_final: 0.8900 (ttmm) REVERT: L 142 MET cc_start: 0.8579 (mtt) cc_final: 0.8279 (mtp) REVERT: L 168 ASP cc_start: 0.8878 (t0) cc_final: 0.8471 (t0) REVERT: L 186 THR cc_start: 0.9290 (t) cc_final: 0.9006 (m) REVERT: L 222 ARG cc_start: 0.8829 (mmt180) cc_final: 0.8489 (mmm160) REVERT: B 387 MET cc_start: 0.8234 (mtt) cc_final: 0.7869 (mtp) REVERT: B 394 LYS cc_start: 0.9370 (ttmt) cc_final: 0.8974 (ttmm) REVERT: B 406 VAL cc_start: 0.8355 (p) cc_final: 0.8090 (t) REVERT: C 112 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7464 (tpp) REVERT: C 133 TYR cc_start: 0.8978 (m-80) cc_final: 0.8690 (m-10) REVERT: C 135 CYS cc_start: 0.8809 (t) cc_final: 0.8587 (t) REVERT: C 136 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8660 (tt) REVERT: C 168 ASP cc_start: 0.8860 (t70) cc_final: 0.8189 (t0) REVERT: C 189 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8786 (pttm) REVERT: C 265 THR cc_start: 0.8873 (OUTLIER) cc_final: 0.8281 (t) REVERT: D 412 ARG cc_start: 0.7708 (mtt180) cc_final: 0.6780 (mpp-170) REVERT: E 388 PHE cc_start: 0.8165 (m-10) cc_final: 0.7849 (m-80) REVERT: E 394 LYS cc_start: 0.9477 (ttmt) cc_final: 0.9060 (ttmm) REVERT: F 156 LEU cc_start: 0.8579 (mp) cc_final: 0.8346 (mt) REVERT: F 189 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.7654 (pmmt) REVERT: F 266 GLU cc_start: 0.7994 (pm20) cc_final: 0.7740 (pm20) REVERT: G 412 ARG cc_start: 0.7634 (mtt180) cc_final: 0.6808 (mpp-170) REVERT: G 417 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7506 (pp) REVERT: H 386 TYR cc_start: 0.8899 (t80) cc_final: 0.8474 (t80) REVERT: H 387 MET cc_start: 0.8449 (mtt) cc_final: 0.8140 (mtp) REVERT: H 394 LYS cc_start: 0.9371 (ttmt) cc_final: 0.8899 (ttmm) REVERT: I 112 MET cc_start: 0.7919 (ttm) cc_final: 0.7517 (tpt) REVERT: I 186 THR cc_start: 0.9488 (t) cc_final: 0.9180 (m) REVERT: I 204 SER cc_start: 0.9332 (t) cc_final: 0.8862 (p) REVERT: I 266 GLU cc_start: 0.7818 (pm20) cc_final: 0.7375 (pm20) REVERT: M 412 ARG cc_start: 0.7584 (mtt180) cc_final: 0.6959 (mpp-170) REVERT: N 386 TYR cc_start: 0.8934 (t80) cc_final: 0.8424 (t80) REVERT: N 387 MET cc_start: 0.8258 (mtp) cc_final: 0.7885 (mtp) REVERT: N 388 PHE cc_start: 0.8405 (m-10) cc_final: 0.8077 (m-80) REVERT: N 394 LYS cc_start: 0.9386 (ttmt) cc_final: 0.9147 (ttmm) REVERT: O 175 PRO cc_start: 0.9505 (Cg_exo) cc_final: 0.9304 (Cg_endo) REVERT: O 266 GLU cc_start: 0.7936 (pm20) cc_final: 0.7663 (pm20) outliers start: 66 outliers final: 49 residues processed: 348 average time/residue: 0.2330 time to fit residues: 108.6442 Evaluate side-chains 354 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 298 time to evaluate : 1.169 ------------------------------------------------------------------------------- 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 165 SER 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 434 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 189 LYS 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 E residue 377 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 F residue 184 LYS Chi-restraints excluded: chain F residue 189 LYS 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 G residue 434 VAL Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain M residue 425 VAL Chi-restraints excluded: chain M residue 427 VAL Chi-restraints excluded: chain M residue 432 THR Chi-restraints excluded: chain M residue 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 88 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9125 Z= 0.336 Angle : 0.697 11.303 12365 Z= 0.357 Chirality : 0.047 0.193 1435 Planarity : 0.007 0.065 1555 Dihedral : 6.756 71.664 1292 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.64 % Favored : 89.36 % Rotamer: Outliers : 8.57 % Allowed : 22.75 % Favored : 68.68 % 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: -3.73 (0.22), residues: 1165 helix: -1.46 (0.28), residues: 320 sheet: -2.46 (0.48), residues: 120 loop : -3.14 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 196 HIS 0.009 0.001 HIS F 146 PHE 0.012 0.002 PHE O 208 TYR 0.017 0.002 TYR F 161 ARG 0.006 0.001 ARG M 437 *********************** 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 381 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 300 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7598 (mtt180) cc_final: 0.6797 (mpp-170) REVERT: J 417 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7254 (pp) REVERT: K 387 MET cc_start: 0.8351 (mtt) cc_final: 0.7938 (mtp) REVERT: K 394 LYS cc_start: 0.9297 (ttmt) cc_final: 0.8882 (ttmm) REVERT: L 168 ASP cc_start: 0.8903 (t0) cc_final: 0.8632 (t0) REVERT: L 186 THR cc_start: 0.9319 (OUTLIER) cc_final: 0.9034 (m) REVERT: A 417 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7621 (pp) REVERT: B 387 MET cc_start: 0.8175 (mtt) cc_final: 0.7830 (mtp) REVERT: B 394 LYS cc_start: 0.9379 (ttmt) cc_final: 0.9017 (ttmm) REVERT: B 406 VAL cc_start: 0.8297 (p) cc_final: 0.8066 (t) REVERT: C 112 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7473 (tpp) REVERT: C 133 TYR cc_start: 0.9066 (m-80) cc_final: 0.8828 (m-10) REVERT: C 135 CYS cc_start: 0.8895 (t) cc_final: 0.8658 (t) REVERT: C 136 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8726 (tt) REVERT: C 168 ASP cc_start: 0.8871 (t70) cc_final: 0.8223 (t0) REVERT: C 189 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8751 (pttm) REVERT: C 265 THR cc_start: 0.8877 (OUTLIER) cc_final: 0.8306 (t) REVERT: D 412 ARG cc_start: 0.7724 (mtt180) cc_final: 0.6791 (mpp-170) REVERT: E 388 PHE cc_start: 0.8188 (m-10) cc_final: 0.7910 (m-80) REVERT: E 394 LYS cc_start: 0.9477 (ttmt) cc_final: 0.9065 (ttmm) REVERT: E 411 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7365 (tp) REVERT: F 112 MET cc_start: 0.7018 (tpp) cc_final: 0.6807 (tpp) REVERT: F 147 VAL cc_start: 0.8327 (t) cc_final: 0.8055 (p) REVERT: F 168 ASP cc_start: 0.8873 (t70) cc_final: 0.8410 (t0) REVERT: F 189 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.7622 (pmmt) REVERT: F 266 GLU cc_start: 0.8052 (pm20) cc_final: 0.7775 (pm20) REVERT: G 412 ARG cc_start: 0.7572 (mtt180) cc_final: 0.6783 (mpp-170) REVERT: G 417 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7640 (pp) REVERT: H 386 TYR cc_start: 0.8956 (t80) cc_final: 0.8536 (t80) REVERT: H 387 MET cc_start: 0.8425 (mtt) cc_final: 0.8141 (mtp) REVERT: H 394 LYS cc_start: 0.9368 (ttmt) cc_final: 0.8867 (ttmm) REVERT: I 112 MET cc_start: 0.7925 (ttm) cc_final: 0.7548 (tpt) REVERT: I 186 THR cc_start: 0.9530 (t) cc_final: 0.9327 (m) REVERT: I 204 SER cc_start: 0.9326 (t) cc_final: 0.8842 (p) REVERT: I 266 GLU cc_start: 0.7844 (pm20) cc_final: 0.7382 (pm20) REVERT: M 412 ARG cc_start: 0.7592 (mtt180) cc_final: 0.6972 (mpp-170) REVERT: N 394 LYS cc_start: 0.9367 (ttmt) cc_final: 0.9100 (ttmm) REVERT: O 216 LYS cc_start: 0.9258 (OUTLIER) cc_final: 0.9040 (ttmm) REVERT: O 266 GLU cc_start: 0.7942 (pm20) cc_final: 0.7660 (pm20) outliers start: 81 outliers final: 59 residues processed: 348 average time/residue: 0.2333 time to fit residues: 107.8443 Evaluate side-chains 362 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 292 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 431 VAL Chi-restraints excluded: chain J residue 432 THR Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain L residue 119 ASP Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain L residue 164 SER Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain L residue 216 LYS Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 434 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 189 LYS 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 434 VAL Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain E residue 411 LEU 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 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 G residue 434 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 137 VAL Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain M residue 425 VAL Chi-restraints excluded: chain M residue 427 VAL Chi-restraints excluded: chain M residue 432 THR Chi-restraints excluded: chain M residue 434 VAL 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 216 LYS 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 35 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 8 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4071 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= 0.172 Angle : 0.614 8.072 12365 Z= 0.311 Chirality : 0.045 0.161 1435 Planarity : 0.007 0.062 1555 Dihedral : 6.657 78.712 1292 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 4.55 % Allowed : 26.77 % Favored : 68.68 % 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: -3.38 (0.23), residues: 1165 helix: -1.20 (0.27), residues: 360 sheet: -2.46 (0.47), residues: 120 loop : -2.93 (0.21), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 268 HIS 0.007 0.001 HIS F 146 PHE 0.008 0.001 PHE H 388 TYR 0.014 0.001 TYR C 161 ARG 0.006 0.000 ARG J 437 *********************** 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: 43 poor density : 312 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7496 (mtt180) cc_final: 0.6709 (mpp-170) REVERT: J 436 MET cc_start: 0.8233 (tmm) cc_final: 0.7926 (tmm) REVERT: K 394 LYS cc_start: 0.9245 (ttmt) cc_final: 0.8879 (ttmm) REVERT: L 142 MET cc_start: 0.8668 (mtt) cc_final: 0.8404 (mtp) REVERT: L 186 THR cc_start: 0.9227 (t) cc_final: 0.8949 (m) REVERT: A 417 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7339 (pp) REVERT: B 387 MET cc_start: 0.8159 (mtt) cc_final: 0.7949 (mtp) REVERT: B 394 LYS cc_start: 0.9329 (ttmt) cc_final: 0.8966 (ttmm) REVERT: B 406 VAL cc_start: 0.8245 (p) cc_final: 0.7869 (t) REVERT: C 136 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8502 (tt) REVERT: C 168 ASP cc_start: 0.8765 (t70) cc_final: 0.8517 (t70) REVERT: C 189 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8746 (pttm) REVERT: C 265 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8307 (t) REVERT: E 388 PHE cc_start: 0.8201 (m-10) cc_final: 0.7898 (m-80) REVERT: E 394 LYS cc_start: 0.9306 (ttmt) cc_final: 0.8937 (ttmm) REVERT: F 112 MET cc_start: 0.7101 (tpp) cc_final: 0.6869 (tpp) REVERT: F 168 ASP cc_start: 0.8835 (t70) cc_final: 0.8222 (t0) REVERT: F 189 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8402 (pttm) REVERT: F 265 THR cc_start: 0.8855 (p) cc_final: 0.8322 (t) REVERT: G 412 ARG cc_start: 0.7477 (mtt180) cc_final: 0.6843 (mpp-170) REVERT: H 386 TYR cc_start: 0.8841 (t80) cc_final: 0.8438 (t80) REVERT: H 394 LYS cc_start: 0.9260 (ttmt) cc_final: 0.8904 (ttmm) REVERT: I 186 THR cc_start: 0.9509 (t) cc_final: 0.9184 (m) REVERT: I 204 SER cc_start: 0.9233 (t) cc_final: 0.8753 (p) REVERT: I 266 GLU cc_start: 0.7774 (pm20) cc_final: 0.7435 (pm20) REVERT: M 412 ARG cc_start: 0.7561 (mtt180) cc_final: 0.6837 (mpp-170) REVERT: N 394 LYS cc_start: 0.9301 (ttmt) cc_final: 0.9072 (ttmm) REVERT: N 406 VAL cc_start: 0.8250 (t) cc_final: 0.7987 (t) REVERT: O 175 PRO cc_start: 0.9432 (Cg_exo) cc_final: 0.9195 (Cg_endo) REVERT: O 186 THR cc_start: 0.9372 (t) cc_final: 0.9154 (m) REVERT: O 204 SER cc_start: 0.9191 (t) cc_final: 0.8602 (p) REVERT: O 216 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.9083 (ttmm) REVERT: O 266 GLU cc_start: 0.7852 (pm20) cc_final: 0.7270 (pm20) outliers start: 43 outliers final: 25 residues processed: 339 average time/residue: 0.2234 time to fit residues: 101.5564 Evaluate side-chains 321 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 290 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 A residue 417 LEU Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 189 LYS 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 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 M residue 425 VAL 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 216 LYS 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 11 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 106 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9125 Z= 0.337 Angle : 0.712 11.094 12365 Z= 0.359 Chirality : 0.048 0.165 1435 Planarity : 0.007 0.063 1555 Dihedral : 6.560 73.487 1292 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 5.50 % Allowed : 26.46 % 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: -3.43 (0.23), residues: 1165 helix: -1.22 (0.29), residues: 325 sheet: -2.47 (0.47), residues: 120 loop : -2.91 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 196 HIS 0.006 0.001 HIS F 146 PHE 0.010 0.002 PHE O 208 TYR 0.021 0.002 TYR F 161 ARG 0.006 0.000 ARG A 437 *********************** 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 352 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 300 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7556 (mtt180) cc_final: 0.6747 (mpp-170) REVERT: K 394 LYS cc_start: 0.9289 (ttmt) cc_final: 0.8917 (ttmm) REVERT: L 142 MET cc_start: 0.8691 (mtt) cc_final: 0.8367 (mtp) REVERT: L 186 THR cc_start: 0.9337 (t) cc_final: 0.9031 (m) REVERT: L 203 TYR cc_start: 0.9200 (t80) cc_final: 0.8681 (t80) REVERT: A 417 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7554 (pp) REVERT: B 387 MET cc_start: 0.8145 (mtt) cc_final: 0.7858 (mtp) REVERT: B 394 LYS cc_start: 0.9357 (ttmt) cc_final: 0.9013 (ttmm) REVERT: B 406 VAL cc_start: 0.8326 (p) cc_final: 0.8073 (t) REVERT: C 136 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8682 (tt) REVERT: C 168 ASP cc_start: 0.8867 (t70) cc_final: 0.8352 (t0) REVERT: C 189 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8722 (pttm) REVERT: C 265 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8308 (t) REVERT: E 388 PHE cc_start: 0.8227 (m-10) cc_final: 0.7971 (m-80) REVERT: E 394 LYS cc_start: 0.9340 (ttmt) cc_final: 0.8963 (ttmm) REVERT: F 168 ASP cc_start: 0.8903 (t70) cc_final: 0.8436 (t0) REVERT: F 189 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.7624 (pmmt) REVERT: F 266 GLU cc_start: 0.7951 (pm20) cc_final: 0.7654 (pm20) REVERT: G 412 ARG cc_start: 0.7585 (mtt180) cc_final: 0.6798 (mpp-170) REVERT: H 386 TYR cc_start: 0.8990 (t80) cc_final: 0.8680 (t80) REVERT: H 394 LYS cc_start: 0.9326 (ttmt) cc_final: 0.8941 (ttmm) REVERT: I 204 SER cc_start: 0.9270 (t) cc_final: 0.8787 (p) REVERT: I 266 GLU cc_start: 0.7807 (pm20) cc_final: 0.7503 (pm20) REVERT: M 412 ARG cc_start: 0.7588 (mtt180) cc_final: 0.6975 (mpp-170) REVERT: N 394 LYS cc_start: 0.9340 (ttmt) cc_final: 0.9085 (ttmm) REVERT: O 266 GLU cc_start: 0.7927 (pm20) cc_final: 0.7650 (pm20) outliers start: 52 outliers final: 36 residues processed: 333 average time/residue: 0.2236 time to fit residues: 99.3172 Evaluate side-chains 332 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 291 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 425 VAL Chi-restraints excluded: chain J residue 432 THR Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain L residue 171 CYS Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 234 ILE 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 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 189 LYS Chi-restraints excluded: chain G residue 425 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 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 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 63 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 101 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9125 Z= 0.245 Angle : 0.663 9.070 12365 Z= 0.337 Chirality : 0.046 0.172 1435 Planarity : 0.007 0.062 1555 Dihedral : 6.557 76.024 1292 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 5.29 % Allowed : 27.94 % Favored : 66.77 % 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: -3.30 (0.23), residues: 1165 helix: -1.12 (0.29), residues: 330 sheet: -2.51 (0.46), residues: 120 loop : -2.80 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 268 HIS 0.006 0.001 HIS F 146 PHE 0.007 0.001 PHE B 388 TYR 0.020 0.001 TYR I 133 ARG 0.011 0.000 ARG A 437 *********************** 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 336 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 286 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7522 (mtt180) cc_final: 0.6718 (mpp-170) REVERT: K 394 LYS cc_start: 0.9263 (ttmt) cc_final: 0.8880 (ttmm) REVERT: L 142 MET cc_start: 0.8677 (mtt) cc_final: 0.8362 (mtp) REVERT: L 186 THR cc_start: 0.9308 (t) cc_final: 0.8998 (m) REVERT: L 203 TYR cc_start: 0.9169 (t80) cc_final: 0.8680 (t80) REVERT: A 417 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7431 (pp) REVERT: B 387 MET cc_start: 0.8108 (mtt) cc_final: 0.7778 (mtp) REVERT: B 394 LYS cc_start: 0.9340 (ttmt) cc_final: 0.8979 (ttmm) REVERT: B 406 VAL cc_start: 0.8239 (p) cc_final: 0.7946 (t) REVERT: C 136 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8512 (tt) REVERT: C 168 ASP cc_start: 0.8853 (t70) cc_final: 0.8250 (t70) REVERT: C 189 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8733 (pttm) REVERT: C 265 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8333 (t) REVERT: E 388 PHE cc_start: 0.8204 (m-10) cc_final: 0.7951 (m-80) REVERT: E 394 LYS cc_start: 0.9301 (ttmt) cc_final: 0.8933 (ttmm) REVERT: E 411 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7161 (tp) REVERT: F 168 ASP cc_start: 0.8862 (t70) cc_final: 0.8380 (t0) REVERT: F 266 GLU cc_start: 0.7987 (pm20) cc_final: 0.7750 (pm20) REVERT: G 412 ARG cc_start: 0.7596 (mtt180) cc_final: 0.6813 (mpp-170) REVERT: H 386 TYR cc_start: 0.8941 (t80) cc_final: 0.8611 (t80) REVERT: H 394 LYS cc_start: 0.9343 (ttmt) cc_final: 0.8977 (ttmm) REVERT: I 112 MET cc_start: 0.7834 (tpt) cc_final: 0.7389 (tpp) REVERT: I 133 TYR cc_start: 0.8816 (m-80) cc_final: 0.8253 (m-80) REVERT: I 204 SER cc_start: 0.9236 (t) cc_final: 0.8734 (p) REVERT: I 266 GLU cc_start: 0.7780 (pm20) cc_final: 0.7465 (pm20) REVERT: M 412 ARG cc_start: 0.7584 (mtt180) cc_final: 0.6948 (mpp-170) REVERT: N 394 LYS cc_start: 0.9314 (ttmt) cc_final: 0.9076 (ttmm) REVERT: O 175 PRO cc_start: 0.9469 (Cg_exo) cc_final: 0.9264 (Cg_endo) REVERT: O 216 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.9049 (ttmm) REVERT: O 266 GLU cc_start: 0.7896 (pm20) cc_final: 0.7637 (pm20) outliers start: 50 outliers final: 41 residues processed: 316 average time/residue: 0.2212 time to fit residues: 93.8403 Evaluate side-chains 329 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 282 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 425 VAL Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 189 LYS Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain G residue 432 THR Chi-restraints excluded: chain H residue 377 VAL Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain M residue 425 VAL Chi-restraints excluded: chain M residue 427 VAL Chi-restraints excluded: chain M residue 432 THR Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain O residue 119 ASP Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 158 LYS Chi-restraints excluded: chain O residue 216 LYS 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 98 optimal weight: 8.9990 chunk 101 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 0.0040 chunk 30 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 64 optimal weight: 0.1980 chunk 104 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.4454 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= 0.172 Angle : 0.607 7.564 12365 Z= 0.310 Chirality : 0.045 0.179 1435 Planarity : 0.006 0.062 1555 Dihedral : 6.435 81.799 1292 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 4.23 % Allowed : 28.89 % Favored : 66.88 % 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: -2.98 (0.23), residues: 1165 helix: -0.83 (0.28), residues: 360 sheet: -2.49 (0.45), residues: 120 loop : -2.64 (0.21), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 196 HIS 0.005 0.001 HIS F 146 PHE 0.004 0.001 PHE I 208 TYR 0.015 0.001 TYR I 203 ARG 0.004 0.000 ARG I 111 *********************** 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 335 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 295 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 394 LYS cc_start: 0.9220 (ttmt) cc_final: 0.8870 (ttmm) REVERT: L 142 MET cc_start: 0.8712 (mtt) cc_final: 0.8438 (mtp) REVERT: L 186 THR cc_start: 0.9218 (t) cc_final: 0.8921 (m) REVERT: L 203 TYR cc_start: 0.9132 (t80) cc_final: 0.8736 (t80) REVERT: B 394 LYS cc_start: 0.9282 (ttmt) cc_final: 0.8921 (ttmm) REVERT: B 406 VAL cc_start: 0.8298 (p) cc_final: 0.7953 (t) REVERT: C 136 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8217 (tt) REVERT: C 168 ASP cc_start: 0.8836 (t70) cc_final: 0.8286 (t70) REVERT: C 189 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8816 (pttm) REVERT: D 436 MET cc_start: 0.8344 (tmm) cc_final: 0.8009 (tmm) REVERT: E 388 PHE cc_start: 0.8183 (m-10) cc_final: 0.7893 (m-80) REVERT: E 394 LYS cc_start: 0.9271 (ttmt) cc_final: 0.8944 (ttmm) REVERT: F 168 ASP cc_start: 0.8833 (t70) cc_final: 0.8379 (t0) REVERT: F 202 GLN cc_start: 0.8384 (pt0) cc_final: 0.8168 (pt0) REVERT: F 265 THR cc_start: 0.8676 (p) cc_final: 0.8254 (t) REVERT: F 266 GLU cc_start: 0.7899 (pm20) cc_final: 0.7651 (pm20) REVERT: H 394 LYS cc_start: 0.9382 (ttmt) cc_final: 0.9032 (ttmm) REVERT: I 112 MET cc_start: 0.7584 (tpt) cc_final: 0.7170 (tpp) REVERT: I 123 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7575 (mt-10) REVERT: I 133 TYR cc_start: 0.8542 (m-80) cc_final: 0.8016 (m-80) REVERT: I 204 SER cc_start: 0.9173 (t) cc_final: 0.8669 (p) REVERT: I 266 GLU cc_start: 0.7711 (pm20) cc_final: 0.7438 (pm20) REVERT: M 412 ARG cc_start: 0.7541 (mtt180) cc_final: 0.6832 (mpp-170) REVERT: N 388 PHE cc_start: 0.8208 (m-80) cc_final: 0.7883 (m-80) REVERT: N 394 LYS cc_start: 0.9261 (ttmt) cc_final: 0.9014 (ttmm) REVERT: O 185 TYR cc_start: 0.9235 (p90) cc_final: 0.9022 (p90) REVERT: O 186 THR cc_start: 0.9333 (t) cc_final: 0.9064 (m) REVERT: O 204 SER cc_start: 0.9099 (t) cc_final: 0.8573 (p) REVERT: O 266 GLU cc_start: 0.7835 (pm20) cc_final: 0.7307 (pm20) outliers start: 40 outliers final: 33 residues processed: 324 average time/residue: 0.2179 time to fit residues: 94.9876 Evaluate side-chains 317 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 282 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 189 LYS 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 F residue 121 ILE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain G residue 432 THR Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain M residue 425 VAL Chi-restraints excluded: chain 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 265 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 100 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 92 optimal weight: 0.0270 chunk 26 optimal weight: 0.2980 overall best weight: 1.8642 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9125 Z= 0.206 Angle : 0.630 8.339 12365 Z= 0.318 Chirality : 0.046 0.184 1435 Planarity : 0.006 0.061 1555 Dihedral : 6.342 80.065 1292 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 3.81 % Allowed : 28.68 % Favored : 67.51 % 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: -2.79 (0.23), residues: 1165 helix: -0.64 (0.29), residues: 340 sheet: -2.46 (0.45), residues: 120 loop : -2.48 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 268 HIS 0.005 0.001 HIS F 146 PHE 0.006 0.001 PHE O 208 TYR 0.015 0.001 TYR I 133 ARG 0.009 0.000 ARG A 437 ********************** 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 319 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 283 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 436 MET cc_start: 0.8300 (tmm) cc_final: 0.8012 (tmm) REVERT: K 394 LYS cc_start: 0.9247 (ttmt) cc_final: 0.8887 (ttmm) REVERT: L 142 MET cc_start: 0.8718 (mtt) cc_final: 0.8441 (mtp) REVERT: L 186 THR cc_start: 0.9271 (t) cc_final: 0.8961 (m) REVERT: L 203 TYR cc_start: 0.9183 (t80) cc_final: 0.8776 (t80) REVERT: B 394 LYS cc_start: 0.9318 (ttmt) cc_final: 0.8962 (ttmm) REVERT: B 406 VAL cc_start: 0.8527 (p) cc_final: 0.8202 (t) REVERT: C 136 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8420 (tt) REVERT: C 168 ASP cc_start: 0.8865 (t70) cc_final: 0.8333 (t70) REVERT: C 169 LEU cc_start: 0.9497 (mt) cc_final: 0.9251 (tp) REVERT: D 436 MET cc_start: 0.8390 (tmm) cc_final: 0.8018 (tmm) REVERT: E 388 PHE cc_start: 0.8146 (m-10) cc_final: 0.7922 (m-80) REVERT: E 394 LYS cc_start: 0.9298 (ttmt) cc_final: 0.8927 (ttmm) REVERT: F 168 ASP cc_start: 0.8877 (t70) cc_final: 0.8444 (t0) REVERT: F 265 THR cc_start: 0.8721 (p) cc_final: 0.8278 (t) REVERT: F 266 GLU cc_start: 0.7931 (pm20) cc_final: 0.7689 (pm20) REVERT: H 394 LYS cc_start: 0.9395 (ttmt) cc_final: 0.9054 (ttmm) REVERT: I 112 MET cc_start: 0.7617 (tpt) cc_final: 0.7223 (tpp) REVERT: I 133 TYR cc_start: 0.8679 (m-80) cc_final: 0.8110 (m-80) REVERT: I 185 TYR cc_start: 0.9262 (p90) cc_final: 0.8843 (p90) REVERT: I 204 SER cc_start: 0.9130 (t) cc_final: 0.8583 (p) REVERT: I 266 GLU cc_start: 0.7746 (pm20) cc_final: 0.7456 (pm20) REVERT: M 412 ARG cc_start: 0.7489 (mtt180) cc_final: 0.6834 (mpp-170) REVERT: N 388 PHE cc_start: 0.8189 (m-80) cc_final: 0.7883 (m-80) REVERT: N 394 LYS cc_start: 0.9282 (ttmt) cc_final: 0.9046 (ttmm) REVERT: O 175 PRO cc_start: 0.9397 (Cg_exo) cc_final: 0.9139 (Cg_endo) REVERT: O 204 SER cc_start: 0.9175 (t) cc_final: 0.8608 (p) REVERT: O 266 GLU cc_start: 0.7834 (pm20) cc_final: 0.7498 (pm20) outliers start: 36 outliers final: 34 residues processed: 307 average time/residue: 0.2148 time to fit residues: 89.1551 Evaluate side-chains 315 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 280 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain G residue 432 THR Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain H residue 411 LEU 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 265 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 76 optimal weight: 0.2980 chunk 4 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.126327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.110386 restraints weight = 14498.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.113543 restraints weight = 7338.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.115734 restraints weight = 4527.673| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9125 Z= 0.202 Angle : 0.629 8.326 12365 Z= 0.317 Chirality : 0.046 0.184 1435 Planarity : 0.006 0.062 1555 Dihedral : 6.267 79.854 1292 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 4.23 % Allowed : 28.78 % 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: -2.72 (0.23), residues: 1165 helix: -0.59 (0.29), residues: 340 sheet: -2.41 (0.44), residues: 120 loop : -2.43 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 268 HIS 0.005 0.001 HIS F 146 PHE 0.007 0.001 PHE B 388 TYR 0.015 0.001 TYR I 133 ARG 0.007 0.000 ARG M 437 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2338.11 seconds wall clock time: 43 minutes 11.36 seconds (2591.36 seconds total)