Starting phenix.real_space_refine on Thu Feb 13 11:46:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wco_32426/02_2025/7wco_32426.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wco_32426/02_2025/7wco_32426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wco_32426/02_2025/7wco_32426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wco_32426/02_2025/7wco_32426.map" model { file = "/net/cci-nas-00/data/ceres_data/7wco_32426/02_2025/7wco_32426.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wco_32426/02_2025/7wco_32426.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 5670 2.51 5 N 1585 2.21 5 O 1615 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 3.73, per 1000 atoms: 0.42 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: 1.96 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: 1.07 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: 2.37 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2875 1.34 - 1.46: 1979 1.46 - 1.58: 4156 1.58 - 1.70: 0 1.70 - 1.82: 115 Bond restraints: 9125 Sorted by residual: bond pdb=" N ALA H 420 " pdb=" CA ALA H 420 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.27e-02 6.20e+03 6.21e+00 bond pdb=" N ALA B 420 " pdb=" CA ALA B 420 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.27e-02 6.20e+03 6.06e+00 bond pdb=" N ALA K 420 " pdb=" CA ALA K 420 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.27e-02 6.20e+03 6.01e+00 bond pdb=" N ALA E 420 " pdb=" CA ALA E 420 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.27e-02 6.20e+03 5.91e+00 bond pdb=" N ALA N 420 " pdb=" CA ALA N 420 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.27e-02 6.20e+03 5.88e+00 ... (remaining 9120 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 11491 2.01 - 4.01: 739 4.01 - 6.02: 95 6.02 - 8.02: 20 8.02 - 10.03: 20 Bond angle restraints: 12365 Sorted by residual: angle pdb=" CA LYS F 158 " pdb=" CB LYS F 158 " pdb=" CG LYS F 158 " ideal model delta sigma weight residual 114.10 122.60 -8.50 2.00e+00 2.50e-01 1.81e+01 angle pdb=" CA LYS C 158 " pdb=" CB LYS C 158 " pdb=" CG LYS C 158 " ideal model delta sigma weight residual 114.10 122.60 -8.50 2.00e+00 2.50e-01 1.80e+01 angle pdb=" CA LYS L 158 " pdb=" CB LYS L 158 " pdb=" CG LYS L 158 " ideal model delta sigma weight residual 114.10 122.60 -8.50 2.00e+00 2.50e-01 1.80e+01 angle pdb=" CA LYS O 158 " pdb=" CB LYS O 158 " pdb=" CG LYS O 158 " ideal model delta sigma weight residual 114.10 122.59 -8.49 2.00e+00 2.50e-01 1.80e+01 angle pdb=" CA LYS I 158 " pdb=" CB LYS I 158 " pdb=" CG LYS I 158 " ideal model delta sigma weight residual 114.10 122.56 -8.46 2.00e+00 2.50e-01 1.79e+01 ... (remaining 12360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 5185 17.02 - 34.04: 195 34.04 - 51.06: 75 51.06 - 68.07: 0 68.07 - 85.09: 5 Dihedral angle restraints: 5460 sinusoidal: 2085 harmonic: 3375 Sorted by residual: dihedral pdb=" CA ARG H 419 " pdb=" C ARG H 419 " pdb=" N ALA H 420 " pdb=" CA ALA H 420 " ideal model delta harmonic sigma weight residual 180.00 131.29 48.71 0 5.00e+00 4.00e-02 9.49e+01 dihedral pdb=" CA ARG K 419 " pdb=" C ARG K 419 " pdb=" N ALA K 420 " pdb=" CA ALA K 420 " ideal model delta harmonic sigma weight residual 180.00 131.31 48.69 0 5.00e+00 4.00e-02 9.48e+01 dihedral pdb=" CA ARG B 419 " pdb=" C ARG B 419 " pdb=" N ALA B 420 " pdb=" CA ALA B 420 " ideal model delta harmonic sigma weight residual 180.00 131.31 48.69 0 5.00e+00 4.00e-02 9.48e+01 ... (remaining 5457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 953 0.054 - 0.108: 368 0.108 - 0.162: 87 0.162 - 0.216: 17 0.216 - 0.270: 10 Chirality restraints: 1435 Sorted by residual: chirality pdb=" CA THR B 397 " pdb=" N THR B 397 " pdb=" C THR B 397 " pdb=" CB THR B 397 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA THR H 397 " pdb=" N THR H 397 " pdb=" C THR H 397 " pdb=" CB THR H 397 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA THR N 397 " pdb=" N THR N 397 " pdb=" C THR N 397 " pdb=" CB THR N 397 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1432 not shown) Planarity restraints: 1555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 435 " -0.030 2.00e-02 2.50e+03 5.80e-02 3.36e+01 pdb=" C THR D 435 " 0.100 2.00e-02 2.50e+03 pdb=" O THR D 435 " -0.037 2.00e-02 2.50e+03 pdb=" N MET D 436 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 435 " -0.030 2.00e-02 2.50e+03 5.80e-02 3.36e+01 pdb=" C THR G 435 " 0.100 2.00e-02 2.50e+03 pdb=" O THR G 435 " -0.037 2.00e-02 2.50e+03 pdb=" N MET G 436 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR J 435 " -0.030 2.00e-02 2.50e+03 5.79e-02 3.35e+01 pdb=" C THR J 435 " 0.100 2.00e-02 2.50e+03 pdb=" O THR J 435 " -0.037 2.00e-02 2.50e+03 pdb=" N MET J 436 " -0.033 2.00e-02 2.50e+03 ... (remaining 1552 not shown) Histogram of nonbonded interaction distances: 0.60 - 1.46: 45 1.46 - 2.32: 80 2.32 - 3.18: 7375 3.18 - 4.04: 20488 4.04 - 4.90: 36824 Warning: very small nonbonded interaction distances. Nonbonded interactions: 64812 Sorted by model distance: nonbonded pdb=" CD1 LEU K 411 " pdb=" CZ ARG A 437 " model vdw 0.599 3.690 nonbonded pdb=" CD1 LEU H 411 " pdb=" CZ ARG M 437 " model vdw 0.599 3.690 nonbonded pdb=" CD1 LEU B 411 " pdb=" CZ ARG D 437 " model vdw 0.600 3.690 nonbonded pdb=" CZ ARG J 437 " pdb=" CD1 LEU N 411 " model vdw 0.600 3.690 nonbonded pdb=" CD1 LEU E 411 " pdb=" CZ ARG G 437 " model vdw 0.600 3.690 ... (remaining 64807 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 20.870 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.370 ------------------------------------------------------------------------------- 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 : 0.902 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: 0.2363 time to fit residues: 112.6774 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 : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain O residue 136 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 202 GLN C 193 HIS C 202 GLN F 202 GLN I 202 GLN O 202 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.128344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.112983 restraints weight = 14806.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.116093 restraints weight = 7634.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.118155 restraints weight = 4778.048| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- 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 : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7435 (mtt180) cc_final: 0.6690 (mpp-170) REVERT: K 387 MET cc_start: 0.8271 (mtt) cc_final: 0.7979 (mtp) REVERT: K 394 LYS cc_start: 0.9295 (ttmt) cc_final: 0.8813 (ttmm) REVERT: L 112 MET cc_start: 0.7523 (ttm) cc_final: 0.7308 (tpt) REVERT: L 142 MET cc_start: 0.8558 (mtt) cc_final: 0.8354 (mtp) REVERT: L 186 THR cc_start: 0.9084 (t) cc_final: 0.8807 (m) REVERT: L 204 SER cc_start: 0.9279 (t) cc_final: 0.8517 (p) REVERT: L 235 VAL cc_start: 0.9707 (t) cc_final: 0.9492 (p) REVERT: A 412 ARG cc_start: 0.7592 (mtt180) cc_final: 0.6914 (mpp-170) REVERT: B 387 MET cc_start: 0.8209 (mtt) cc_final: 0.7885 (mtp) REVERT: B 394 LYS cc_start: 0.9319 (ttmt) cc_final: 0.8862 (ttmm) REVERT: C 133 TYR cc_start: 0.8793 (m-80) cc_final: 0.8585 (m-80) REVERT: C 135 CYS cc_start: 0.8790 (t) cc_final: 0.8547 (t) REVERT: C 168 ASP cc_start: 0.8837 (t70) cc_final: 0.8298 (t70) REVERT: C 186 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.8909 (m) REVERT: C 265 THR cc_start: 0.8762 (p) cc_final: 0.8254 (t) REVERT: D 412 ARG cc_start: 0.7521 (mtt180) cc_final: 0.6592 (mpp-170) REVERT: E 394 LYS cc_start: 0.9455 (ttmt) cc_final: 0.9018 (ttmm) REVERT: F 111 ARG cc_start: 0.6818 (ptt-90) cc_final: 0.6611 (ptt90) REVERT: F 112 MET cc_start: 0.7508 (ttm) cc_final: 0.7298 (tpp) REVERT: F 153 ASN cc_start: 0.9026 (t0) cc_final: 0.8575 (t0) REVERT: F 156 LEU cc_start: 0.8556 (mp) cc_final: 0.8245 (mt) REVERT: F 204 SER cc_start: 0.9060 (t) cc_final: 0.8321 (p) REVERT: F 240 ASN cc_start: 0.9176 (t0) cc_final: 0.8929 (t0) REVERT: F 265 THR cc_start: 0.8830 (p) cc_final: 0.8574 (t) REVERT: G 412 ARG cc_start: 0.7698 (mtt180) cc_final: 0.6909 (mpp-170) REVERT: H 386 TYR cc_start: 0.8772 (t80) cc_final: 0.8420 (t80) REVERT: H 387 MET cc_start: 0.8333 (mtt) cc_final: 0.8125 (mtp) REVERT: H 394 LYS cc_start: 0.9311 (ttmt) cc_final: 0.8946 (ttmm) REVERT: I 152 ASP cc_start: 0.8215 (t0) cc_final: 0.7956 (t0) REVERT: I 168 ASP cc_start: 0.8918 (t70) cc_final: 0.8665 (t0) REVERT: I 185 TYR cc_start: 0.9183 (p90) cc_final: 0.8968 (p90) REVERT: I 204 SER cc_start: 0.9238 (t) cc_final: 0.8582 (p) REVERT: I 266 GLU cc_start: 0.7805 (pm20) cc_final: 0.7503 (pm20) REVERT: M 412 ARG cc_start: 0.7488 (mtt180) cc_final: 0.6702 (mpp-170) REVERT: N 394 LYS cc_start: 0.9312 (ttmt) cc_final: 0.9026 (ttmm) REVERT: O 204 SER cc_start: 0.9108 (t) cc_final: 0.8495 (p) REVERT: O 240 ASN cc_start: 0.9123 (t0) cc_final: 0.8865 (t0) REVERT: O 266 GLU cc_start: 0.7803 (pm20) cc_final: 0.7532 (pm20) REVERT: O 268 TRP cc_start: 0.8818 (m-10) cc_final: 0.8361 (m-10) outliers start: 46 outliers final: 20 residues processed: 365 average time/residue: 0.2294 time to fit residues: 111.1411 Evaluate side-chains 329 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 308 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 425 VAL Chi-restraints excluded: chain L residue 119 ASP Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain M residue 425 VAL Chi-restraints excluded: chain O residue 119 ASP Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 158 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 78 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.3421 r_free = 0.3421 target = 0.126326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.110946 restraints weight = 15103.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.114018 restraints weight = 7738.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.116123 restraints weight = 4818.264| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9125 Z= 0.259 Angle : 0.669 9.638 12365 Z= 0.344 Chirality : 0.046 0.161 1435 Planarity : 0.007 0.064 1555 Dihedral : 7.004 76.093 1292 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 6.35 % Allowed : 17.99 % Favored : 75.66 % 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: -4.18 (0.21), residues: 1165 helix: -2.32 (0.23), residues: 345 sheet: -2.85 (0.43), residues: 120 loop : -3.14 (0.20), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP O 196 HIS 0.003 0.001 HIS C 193 PHE 0.009 0.001 PHE I 208 TYR 0.020 0.002 TYR F 161 ARG 0.005 0.000 ARG B 393 *********************** 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: 60 poor density : 310 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7524 (mtt180) cc_final: 0.6806 (mpp-170) REVERT: K 387 MET cc_start: 0.8342 (mtt) cc_final: 0.7969 (mtp) REVERT: K 394 LYS cc_start: 0.9383 (ttmt) cc_final: 0.8895 (ttmm) REVERT: L 142 MET cc_start: 0.8544 (mtt) cc_final: 0.8289 (mtp) REVERT: L 168 ASP cc_start: 0.8777 (t0) cc_final: 0.8376 (t0) REVERT: L 186 THR cc_start: 0.9203 (t) cc_final: 0.8986 (m) REVERT: B 387 MET cc_start: 0.8252 (mtt) cc_final: 0.7925 (mtp) REVERT: B 394 LYS cc_start: 0.9378 (ttmt) cc_final: 0.9022 (ttmm) REVERT: C 112 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.7105 (tpp) REVERT: C 133 TYR cc_start: 0.8900 (m-80) cc_final: 0.8683 (m-80) REVERT: C 135 CYS cc_start: 0.8851 (t) cc_final: 0.8635 (t) REVERT: C 136 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8593 (tt) REVERT: C 168 ASP cc_start: 0.8858 (t70) cc_final: 0.8168 (t70) REVERT: C 189 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8871 (pttm) REVERT: C 265 THR cc_start: 0.8860 (p) cc_final: 0.8288 (t) REVERT: D 412 ARG cc_start: 0.7558 (mtt180) cc_final: 0.6647 (mpp-170) REVERT: E 394 LYS cc_start: 0.9383 (ttmt) cc_final: 0.8921 (ttmm) REVERT: F 156 LEU cc_start: 0.8625 (mp) cc_final: 0.8360 (mp) REVERT: F 168 ASP cc_start: 0.8785 (t70) cc_final: 0.8232 (t70) REVERT: F 189 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.7720 (pmmt) REVERT: F 204 SER cc_start: 0.9157 (t) cc_final: 0.8585 (p) REVERT: F 240 ASN cc_start: 0.9146 (t0) cc_final: 0.8900 (t0) REVERT: F 265 THR cc_start: 0.8884 (p) cc_final: 0.8367 (t) REVERT: G 412 ARG cc_start: 0.7639 (mtt180) cc_final: 0.6869 (mpp-170) REVERT: H 386 TYR cc_start: 0.8838 (t80) cc_final: 0.8442 (t80) REVERT: H 387 MET cc_start: 0.8389 (mtt) cc_final: 0.8188 (mtp) REVERT: H 394 LYS cc_start: 0.9407 (ttmt) cc_final: 0.8889 (ttmm) REVERT: I 112 MET cc_start: 0.7541 (ttm) cc_final: 0.7308 (tpt) REVERT: I 152 ASP cc_start: 0.8106 (t0) cc_final: 0.7891 (t0) REVERT: I 204 SER cc_start: 0.9342 (t) cc_final: 0.8834 (p) REVERT: I 266 GLU cc_start: 0.7807 (pm20) cc_final: 0.7460 (pm20) REVERT: M 412 ARG cc_start: 0.7637 (mtt180) cc_final: 0.6951 (mpp-170) REVERT: N 388 PHE cc_start: 0.8399 (m-10) cc_final: 0.8183 (m-10) REVERT: N 394 LYS cc_start: 0.9367 (ttmt) cc_final: 0.9074 (ttmm) REVERT: O 204 SER cc_start: 0.9150 (t) cc_final: 0.8638 (p) REVERT: O 266 GLU cc_start: 0.7872 (pm20) cc_final: 0.7655 (pm20) REVERT: O 268 TRP cc_start: 0.8908 (m-10) cc_final: 0.8641 (m-10) outliers start: 60 outliers final: 42 residues processed: 346 average time/residue: 0.2533 time to fit residues: 115.2939 Evaluate side-chains 347 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 301 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 425 VAL Chi-restraints excluded: chain J residue 427 VAL Chi-restraints excluded: chain J residue 432 THR Chi-restraints excluded: chain J residue 437 ARG Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain L residue 119 ASP Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain L residue 165 SER Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain 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 F residue 119 ASP Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 189 LYS Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain G residue 427 VAL Chi-restraints excluded: chain G residue 432 THR Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain I residue 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 411 LEU Chi-restraints excluded: chain O residue 119 ASP Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 158 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 23 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 8 optimal weight: 0.0470 chunk 13 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.123961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.108646 restraints weight = 14892.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.111697 restraints weight = 7594.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.113785 restraints weight = 4731.999| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9125 Z= 0.253 Angle : 0.653 10.324 12365 Z= 0.334 Chirality : 0.046 0.167 1435 Planarity : 0.007 0.063 1555 Dihedral : 6.826 75.777 1292 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 6.14 % Allowed : 22.75 % Favored : 71.11 % 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: -3.77 (0.22), residues: 1165 helix: -1.67 (0.27), residues: 320 sheet: -2.65 (0.46), residues: 120 loop : -3.04 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 196 HIS 0.005 0.001 HIS L 146 PHE 0.008 0.001 PHE O 208 TYR 0.017 0.002 TYR F 161 ARG 0.010 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 359 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 301 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7547 (mtt180) cc_final: 0.6840 (mpp-170) REVERT: J 417 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7242 (pp) REVERT: K 387 MET cc_start: 0.8322 (mtt) cc_final: 0.7975 (mtp) REVERT: K 394 LYS cc_start: 0.9367 (ttmt) cc_final: 0.8916 (ttmm) REVERT: L 112 MET cc_start: 0.7748 (tpt) cc_final: 0.7451 (tpp) REVERT: L 142 MET cc_start: 0.8485 (mtt) cc_final: 0.8207 (mtp) REVERT: L 168 ASP cc_start: 0.8799 (t0) cc_final: 0.8513 (t0) REVERT: L 186 THR cc_start: 0.9235 (t) cc_final: 0.8960 (m) REVERT: A 417 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7254 (pp) REVERT: B 387 MET cc_start: 0.8151 (mtt) cc_final: 0.7829 (mtp) REVERT: B 394 LYS cc_start: 0.9358 (ttmt) cc_final: 0.8988 (ttmm) REVERT: C 112 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.7221 (tpp) REVERT: C 133 TYR cc_start: 0.8918 (m-80) cc_final: 0.8626 (m-10) REVERT: C 136 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8668 (tt) REVERT: C 168 ASP cc_start: 0.8820 (t70) cc_final: 0.8176 (t70) REVERT: C 189 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8819 (pttm) REVERT: C 265 THR cc_start: 0.8854 (p) cc_final: 0.8307 (t) REVERT: D 412 ARG cc_start: 0.7579 (mtt180) cc_final: 0.6685 (mpp-170) REVERT: E 394 LYS cc_start: 0.9477 (ttmt) cc_final: 0.9067 (ttmm) REVERT: F 168 ASP cc_start: 0.8848 (t70) cc_final: 0.8292 (t70) REVERT: F 265 THR cc_start: 0.8869 (p) cc_final: 0.8361 (t) REVERT: G 412 ARG cc_start: 0.7627 (mtt180) cc_final: 0.6865 (mpp-170) REVERT: G 417 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7366 (pp) REVERT: H 386 TYR cc_start: 0.8848 (t80) cc_final: 0.8472 (t80) REVERT: H 394 LYS cc_start: 0.9380 (ttmt) cc_final: 0.8861 (ttmm) REVERT: I 112 MET cc_start: 0.7589 (ttm) cc_final: 0.7385 (tpt) REVERT: I 152 ASP cc_start: 0.7986 (t0) cc_final: 0.7784 (t0) REVERT: I 186 THR cc_start: 0.9451 (t) cc_final: 0.9131 (m) REVERT: I 204 SER cc_start: 0.9352 (t) cc_final: 0.8885 (p) REVERT: I 266 GLU cc_start: 0.7788 (pm20) cc_final: 0.7474 (pm20) REVERT: M 412 ARG cc_start: 0.7643 (mtt180) cc_final: 0.6986 (mpp-170) REVERT: N 394 LYS cc_start: 0.9359 (ttmt) cc_final: 0.9106 (ttmm) REVERT: O 204 SER cc_start: 0.9194 (t) cc_final: 0.8652 (p) REVERT: O 266 GLU cc_start: 0.7881 (pm20) cc_final: 0.7651 (pm20) outliers start: 58 outliers final: 45 residues processed: 340 average time/residue: 0.2327 time to fit residues: 105.3577 Evaluate side-chains 340 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 289 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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 J residue 437 ARG Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain L residue 164 SER Chi-restraints excluded: chain A residue 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 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 D residue 417 LEU Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 189 LYS Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain G residue 427 VAL Chi-restraints excluded: chain G residue 432 THR Chi-restraints excluded: chain H residue 411 LEU 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 411 LEU Chi-restraints excluded: chain O residue 119 ASP Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 158 LYS Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain O residue 265 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 1.9990 chunk 82 optimal weight: 0.0980 chunk 62 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- 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 = 0.3373 r_free = 0.3373 target = 0.121712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.106445 restraints weight = 14920.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.109429 restraints weight = 7575.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.111474 restraints weight = 4689.677| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3703 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= 0.296 Angle : 0.679 11.218 12365 Z= 0.344 Chirality : 0.047 0.186 1435 Planarity : 0.007 0.064 1555 Dihedral : 6.709 74.028 1292 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 6.77 % Allowed : 23.17 % Favored : 70.05 % 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: -3.61 (0.22), residues: 1165 helix: -1.41 (0.28), residues: 320 sheet: -2.50 (0.47), residues: 120 loop : -3.01 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 196 HIS 0.003 0.001 HIS I 193 PHE 0.011 0.002 PHE O 208 TYR 0.018 0.002 TYR I 133 ARG 0.008 0.001 ARG D 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 365 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 301 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7536 (mtt180) cc_final: 0.6807 (mpp-170) REVERT: J 417 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7355 (pp) REVERT: K 387 MET cc_start: 0.8234 (mtt) cc_final: 0.7864 (mtp) REVERT: K 394 LYS cc_start: 0.9300 (ttmt) cc_final: 0.8878 (ttmm) REVERT: L 112 MET cc_start: 0.7774 (tpt) cc_final: 0.7395 (tpp) REVERT: L 186 THR cc_start: 0.9262 (t) cc_final: 0.8986 (m) REVERT: B 387 MET cc_start: 0.8091 (mtt) cc_final: 0.7759 (mtp) REVERT: B 394 LYS cc_start: 0.9369 (ttmt) cc_final: 0.8974 (ttmm) REVERT: C 112 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.7226 (tpp) REVERT: C 133 TYR cc_start: 0.8945 (m-80) cc_final: 0.8662 (m-10) REVERT: C 136 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8649 (tt) REVERT: C 168 ASP cc_start: 0.8846 (t70) cc_final: 0.8281 (t70) REVERT: C 189 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8787 (pttm) REVERT: C 265 THR cc_start: 0.8829 (OUTLIER) cc_final: 0.8305 (t) REVERT: C 268 TRP cc_start: 0.8788 (m-10) cc_final: 0.8550 (m-10) REVERT: D 412 ARG cc_start: 0.7709 (mtt180) cc_final: 0.6834 (mpp-170) REVERT: E 394 LYS cc_start: 0.9473 (ttmt) cc_final: 0.9075 (ttmm) REVERT: E 411 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7505 (tp) REVERT: F 189 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.7645 (pmmt) REVERT: F 266 GLU cc_start: 0.7976 (pm20) cc_final: 0.7689 (pm20) REVERT: G 412 ARG cc_start: 0.7565 (mtt180) cc_final: 0.6841 (mpp-170) REVERT: G 417 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7641 (pp) REVERT: H 386 TYR cc_start: 0.8960 (t80) cc_final: 0.8462 (t80) REVERT: H 394 LYS cc_start: 0.9392 (ttmt) cc_final: 0.8883 (ttmm) REVERT: I 123 GLU cc_start: 0.8255 (mt-10) cc_final: 0.8049 (mt-10) REVERT: I 133 TYR cc_start: 0.8751 (m-80) cc_final: 0.8526 (m-80) REVERT: I 186 THR cc_start: 0.9509 (t) cc_final: 0.9220 (m) REVERT: I 204 SER cc_start: 0.9312 (t) cc_final: 0.8826 (p) REVERT: I 266 GLU cc_start: 0.7808 (pm20) cc_final: 0.7492 (pm20) REVERT: M 412 ARG cc_start: 0.7598 (mtt180) cc_final: 0.7018 (mpp-170) REVERT: N 394 LYS cc_start: 0.9351 (ttmt) cc_final: 0.9100 (ttmm) REVERT: O 266 GLU cc_start: 0.7897 (pm20) cc_final: 0.7659 (pm20) outliers start: 64 outliers final: 48 residues processed: 341 average time/residue: 0.2229 time to fit residues: 101.1896 Evaluate side-chains 345 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 289 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 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 216 LYS Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain B residue 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 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 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 165 SER Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 189 LYS Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain G residue 427 VAL Chi-restraints excluded: chain G residue 432 THR Chi-restraints excluded: chain H residue 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 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 164 SER Chi-restraints excluded: chain O residue 265 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 85 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.123051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.107642 restraints weight = 14785.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.110660 restraints weight = 7477.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.112727 restraints weight = 4630.956| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9125 Z= 0.244 Angle : 0.648 9.283 12365 Z= 0.329 Chirality : 0.046 0.188 1435 Planarity : 0.007 0.063 1555 Dihedral : 6.641 74.742 1292 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 6.67 % Allowed : 24.44 % Favored : 68.89 % 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: -1.21 (0.29), residues: 325 sheet: -2.47 (0.47), residues: 120 loop : -2.92 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 196 HIS 0.014 0.001 HIS F 146 PHE 0.008 0.001 PHE O 208 TYR 0.021 0.002 TYR I 133 ARG 0.004 0.000 ARG M 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 364 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 301 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7526 (mtt180) cc_final: 0.6774 (mpp-170) REVERT: J 417 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7266 (pp) REVERT: K 387 MET cc_start: 0.8189 (mtt) cc_final: 0.7809 (mtp) REVERT: K 394 LYS cc_start: 0.9246 (ttmt) cc_final: 0.8844 (ttmm) REVERT: L 112 MET cc_start: 0.7756 (tpt) cc_final: 0.7389 (tpp) REVERT: L 142 MET cc_start: 0.8685 (mtt) cc_final: 0.8459 (mtp) REVERT: L 186 THR cc_start: 0.9265 (t) cc_final: 0.8981 (m) REVERT: L 203 TYR cc_start: 0.9102 (t80) cc_final: 0.8607 (t80) REVERT: A 417 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7507 (pp) REVERT: B 387 MET cc_start: 0.8066 (mtt) cc_final: 0.7752 (mtp) REVERT: B 394 LYS cc_start: 0.9350 (ttmt) cc_final: 0.8964 (ttmm) REVERT: C 133 TYR cc_start: 0.9015 (m-80) cc_final: 0.8788 (m-10) REVERT: C 136 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8597 (tt) REVERT: C 168 ASP cc_start: 0.8848 (t70) cc_final: 0.8312 (t70) REVERT: C 189 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8786 (pttm) REVERT: C 265 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8312 (t) REVERT: E 394 LYS cc_start: 0.9452 (ttmt) cc_final: 0.9061 (ttmm) REVERT: F 266 GLU cc_start: 0.7952 (pm20) cc_final: 0.7698 (pm20) REVERT: G 412 ARG cc_start: 0.7547 (mtt180) cc_final: 0.6887 (mpp-170) REVERT: G 417 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7579 (pp) REVERT: H 386 TYR cc_start: 0.8894 (t80) cc_final: 0.8549 (t80) REVERT: H 394 LYS cc_start: 0.9348 (ttmt) cc_final: 0.8876 (ttmm) REVERT: I 133 TYR cc_start: 0.8744 (m-80) cc_final: 0.8326 (m-80) REVERT: I 186 THR cc_start: 0.9517 (t) cc_final: 0.9213 (m) REVERT: I 204 SER cc_start: 0.9251 (t) cc_final: 0.8743 (p) REVERT: I 266 GLU cc_start: 0.7809 (pm20) cc_final: 0.7500 (pm20) REVERT: M 412 ARG cc_start: 0.7578 (mtt180) cc_final: 0.6986 (mpp-170) REVERT: N 394 LYS cc_start: 0.9341 (ttmt) cc_final: 0.9061 (ttmm) REVERT: O 186 THR cc_start: 0.9387 (t) cc_final: 0.9172 (m) REVERT: O 266 GLU cc_start: 0.7886 (pm20) cc_final: 0.7620 (pm20) outliers start: 63 outliers final: 47 residues processed: 339 average time/residue: 0.2322 time to fit residues: 104.9434 Evaluate side-chains 341 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 288 time to evaluate : 1.099 ------------------------------------------------------------------------------- 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 L residue 124 VAL 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 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 415 CYS Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 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 D residue 427 VAL Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain F residue 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 193 HIS Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain G residue 427 VAL Chi-restraints excluded: chain G residue 432 THR Chi-restraints excluded: chain H residue 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 67 optimal weight: 8.9990 chunk 84 optimal weight: 0.0270 chunk 64 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 50 optimal weight: 0.0970 chunk 106 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 overall best weight: 1.5638 ------------------------------------------------------------------------------- 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 = 0.3421 r_free = 0.3421 target = 0.125253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.109569 restraints weight = 14573.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.112713 restraints weight = 7264.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.114872 restraints weight = 4427.978| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4122 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= 0.197 Angle : 0.629 7.848 12365 Z= 0.318 Chirality : 0.045 0.194 1435 Planarity : 0.007 0.063 1555 Dihedral : 6.529 76.133 1292 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 5.71 % Allowed : 25.61 % 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: -3.17 (0.23), residues: 1165 helix: -1.00 (0.29), residues: 340 sheet: -2.48 (0.47), residues: 120 loop : -2.74 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 268 HIS 0.011 0.001 HIS F 146 PHE 0.008 0.001 PHE E 388 TYR 0.018 0.001 TYR I 133 ARG 0.007 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 359 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 305 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7542 (mtt180) cc_final: 0.6825 (mpp-170) REVERT: J 436 MET cc_start: 0.8147 (tmm) cc_final: 0.7821 (tmm) REVERT: K 394 LYS cc_start: 0.9226 (ttmt) cc_final: 0.8881 (ttmm) REVERT: L 112 MET cc_start: 0.7734 (tpt) cc_final: 0.7300 (tpp) REVERT: L 186 THR cc_start: 0.9242 (t) cc_final: 0.8951 (m) REVERT: L 203 TYR cc_start: 0.9070 (t80) cc_final: 0.8636 (t80) REVERT: A 417 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7376 (pp) REVERT: B 387 MET cc_start: 0.7978 (mtt) cc_final: 0.7663 (mtp) REVERT: B 388 PHE cc_start: 0.8442 (m-10) cc_final: 0.8170 (m-80) REVERT: B 394 LYS cc_start: 0.9322 (ttmt) cc_final: 0.8948 (ttmm) REVERT: C 136 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8523 (tt) REVERT: C 168 ASP cc_start: 0.8838 (t70) cc_final: 0.8298 (t70) REVERT: C 189 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8791 (pttm) REVERT: C 265 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8288 (t) REVERT: E 394 LYS cc_start: 0.9346 (ttmt) cc_final: 0.9017 (ttmm) REVERT: E 411 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7289 (tp) REVERT: F 153 ASN cc_start: 0.8945 (t0) cc_final: 0.8703 (t0) REVERT: F 189 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8372 (pttm) REVERT: F 265 THR cc_start: 0.8764 (p) cc_final: 0.8252 (t) REVERT: F 266 GLU cc_start: 0.7925 (pm20) cc_final: 0.7677 (pm20) REVERT: G 412 ARG cc_start: 0.7456 (mtt180) cc_final: 0.6867 (mpp-170) REVERT: H 394 LYS cc_start: 0.9301 (ttmt) cc_final: 0.8909 (ttmm) REVERT: I 112 MET cc_start: 0.7472 (tpt) cc_final: 0.7097 (tpp) REVERT: I 133 TYR cc_start: 0.8734 (m-80) cc_final: 0.8230 (m-80) REVERT: I 186 THR cc_start: 0.9508 (t) cc_final: 0.9183 (m) REVERT: I 204 SER cc_start: 0.9189 (t) cc_final: 0.8692 (p) REVERT: I 266 GLU cc_start: 0.7777 (pm20) cc_final: 0.7469 (pm20) REVERT: M 412 ARG cc_start: 0.7572 (mtt180) cc_final: 0.6881 (mpp-170) REVERT: N 394 LYS cc_start: 0.9291 (ttmt) cc_final: 0.9065 (ttmm) REVERT: O 186 THR cc_start: 0.9374 (t) cc_final: 0.9140 (m) REVERT: O 204 SER cc_start: 0.9169 (t) cc_final: 0.8647 (p) REVERT: O 266 GLU cc_start: 0.7838 (pm20) cc_final: 0.7594 (pm20) outliers start: 54 outliers final: 36 residues processed: 336 average time/residue: 0.2222 time to fit residues: 100.6568 Evaluate side-chains 336 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 294 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 124 VAL 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 A residue 417 LEU Chi-restraints excluded: chain A residue 425 VAL 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 D residue 436 MET Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 189 LYS Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain 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 131 THR Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain M residue 425 VAL Chi-restraints excluded: chain M residue 432 THR Chi-restraints excluded: chain 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 32 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 39 optimal weight: 0.0010 chunk 69 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 5 optimal weight: 0.0670 chunk 52 optimal weight: 3.9990 overall best weight: 2.2130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.125207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.109288 restraints weight = 14896.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.112424 restraints weight = 7495.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.114593 restraints weight = 4616.668| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9125 Z= 0.222 Angle : 0.637 8.118 12365 Z= 0.320 Chirality : 0.046 0.160 1435 Planarity : 0.007 0.062 1555 Dihedral : 6.432 74.692 1292 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 5.19 % Allowed : 27.20 % Favored : 67.62 % 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: -3.17 (0.23), residues: 1165 helix: -1.00 (0.29), residues: 330 sheet: -2.48 (0.46), residues: 120 loop : -2.72 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 196 HIS 0.009 0.001 HIS F 146 PHE 0.007 0.001 PHE O 208 TYR 0.017 0.001 TYR L 203 ARG 0.010 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 341 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 292 time to evaluate : 1.005 Fit side-chains REVERT: J 412 ARG cc_start: 0.7549 (mtt180) cc_final: 0.6805 (mpp-170) REVERT: J 436 MET cc_start: 0.8248 (tmm) cc_final: 0.7944 (tmm) REVERT: K 394 LYS cc_start: 0.9250 (ttmt) cc_final: 0.8876 (ttmm) REVERT: L 186 THR cc_start: 0.9273 (t) cc_final: 0.8974 (m) REVERT: L 203 TYR cc_start: 0.9124 (t80) cc_final: 0.8705 (t80) REVERT: A 417 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7490 (pp) REVERT: B 387 MET cc_start: 0.8009 (mtt) cc_final: 0.7663 (mtp) REVERT: B 388 PHE cc_start: 0.8446 (m-10) cc_final: 0.8174 (m-80) REVERT: B 394 LYS cc_start: 0.9323 (ttmt) cc_final: 0.8978 (ttmm) REVERT: C 136 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8581 (tt) REVERT: C 168 ASP cc_start: 0.8841 (t70) cc_final: 0.8302 (t70) REVERT: C 189 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8783 (pttm) REVERT: C 265 THR cc_start: 0.8756 (OUTLIER) cc_final: 0.8315 (t) REVERT: E 394 LYS cc_start: 0.9309 (ttmt) cc_final: 0.8948 (ttmm) REVERT: E 411 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7215 (tp) REVERT: F 168 ASP cc_start: 0.8887 (t70) cc_final: 0.8514 (t0) REVERT: F 189 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8359 (pttm) REVERT: F 265 THR cc_start: 0.8814 (p) cc_final: 0.8257 (t) REVERT: F 266 GLU cc_start: 0.7994 (pm20) cc_final: 0.7733 (pm20) REVERT: G 412 ARG cc_start: 0.7454 (mtt180) cc_final: 0.6851 (mpp-170) REVERT: H 394 LYS cc_start: 0.9306 (ttmt) cc_final: 0.8928 (ttmm) REVERT: I 112 MET cc_start: 0.7402 (tpt) cc_final: 0.7084 (tpp) REVERT: I 133 TYR cc_start: 0.8832 (m-80) cc_final: 0.8344 (m-80) REVERT: I 186 THR cc_start: 0.9510 (t) cc_final: 0.9191 (m) REVERT: I 204 SER cc_start: 0.9237 (t) cc_final: 0.8772 (p) REVERT: I 266 GLU cc_start: 0.7759 (pm20) cc_final: 0.7466 (pm20) REVERT: M 412 ARG cc_start: 0.7496 (mtt180) cc_final: 0.6877 (mpp-170) REVERT: N 388 PHE cc_start: 0.8203 (m-80) cc_final: 0.7888 (m-80) REVERT: N 394 LYS cc_start: 0.9300 (ttmt) cc_final: 0.9039 (ttmm) REVERT: O 114 MET cc_start: 0.7255 (pmt) cc_final: 0.6930 (pmt) REVERT: O 186 THR cc_start: 0.9397 (t) cc_final: 0.9164 (m) REVERT: O 204 SER cc_start: 0.9194 (t) cc_final: 0.8705 (p) REVERT: O 266 GLU cc_start: 0.7862 (pm20) cc_final: 0.7611 (pm20) outliers start: 49 outliers final: 37 residues processed: 320 average time/residue: 0.2227 time to fit residues: 95.7596 Evaluate side-chains 328 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 285 time to evaluate : 1.331 ------------------------------------------------------------------------------- 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 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 425 VAL Chi-restraints excluded: chain A residue 427 VAL 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 D residue 436 MET Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 165 SER 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 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 131 THR Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain M residue 425 VAL Chi-restraints excluded: chain M residue 432 THR Chi-restraints excluded: chain 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 39 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3448 r_free = 0.3448 target = 0.127656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.111687 restraints weight = 14435.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.114869 restraints weight = 7230.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.117063 restraints weight = 4413.140| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4385 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= 0.186 Angle : 0.625 7.809 12365 Z= 0.315 Chirality : 0.045 0.162 1435 Planarity : 0.006 0.062 1555 Dihedral : 6.424 76.626 1292 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 4.76 % Allowed : 27.62 % Favored : 67.62 % 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: -2.95 (0.23), residues: 1165 helix: -0.88 (0.29), residues: 340 sheet: -2.48 (0.45), residues: 120 loop : -2.53 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 196 HIS 0.008 0.001 HIS F 146 PHE 0.007 0.001 PHE E 388 TYR 0.017 0.001 TYR L 203 ARG 0.008 0.000 ARG J 437 *********************** 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 340 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 295 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: K 394 LYS cc_start: 0.9205 (ttmt) cc_final: 0.8824 (ttmm) REVERT: L 112 MET cc_start: 0.7643 (tpt) cc_final: 0.7170 (tpp) REVERT: L 186 THR cc_start: 0.9251 (t) cc_final: 0.8955 (m) REVERT: L 203 TYR cc_start: 0.9131 (t80) cc_final: 0.8735 (t80) REVERT: B 388 PHE cc_start: 0.8428 (m-10) cc_final: 0.8154 (m-80) REVERT: B 394 LYS cc_start: 0.9284 (ttmt) cc_final: 0.8935 (ttmm) REVERT: C 136 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8419 (tt) REVERT: C 168 ASP cc_start: 0.8834 (t70) cc_final: 0.8281 (t70) REVERT: C 189 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8826 (pttm) REVERT: C 265 THR cc_start: 0.8732 (OUTLIER) cc_final: 0.8298 (t) REVERT: E 394 LYS cc_start: 0.9320 (ttmt) cc_final: 0.8972 (ttmm) REVERT: F 189 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8374 (pttm) REVERT: F 265 THR cc_start: 0.8662 (p) cc_final: 0.8266 (t) REVERT: F 266 GLU cc_start: 0.7932 (pm20) cc_final: 0.7675 (pm20) REVERT: H 394 LYS cc_start: 0.9290 (ttmt) cc_final: 0.8946 (ttmm) REVERT: I 112 MET cc_start: 0.7334 (tpt) cc_final: 0.6996 (tpp) REVERT: I 133 TYR cc_start: 0.8793 (m-80) cc_final: 0.8357 (m-80) REVERT: I 186 THR cc_start: 0.9500 (t) cc_final: 0.9285 (m) REVERT: I 204 SER cc_start: 0.9190 (t) cc_final: 0.8691 (p) REVERT: I 266 GLU cc_start: 0.7729 (pm20) cc_final: 0.7475 (pm20) REVERT: M 412 ARG cc_start: 0.7551 (mtt180) cc_final: 0.6863 (mpp-170) REVERT: N 388 PHE cc_start: 0.8188 (m-10) cc_final: 0.7869 (m-80) REVERT: N 394 LYS cc_start: 0.9240 (ttmt) cc_final: 0.9005 (ttmm) REVERT: O 114 MET cc_start: 0.7273 (pmt) cc_final: 0.6956 (pmt) REVERT: O 186 THR cc_start: 0.9386 (t) cc_final: 0.9145 (m) REVERT: O 204 SER cc_start: 0.9252 (t) cc_final: 0.8728 (p) REVERT: O 266 GLU cc_start: 0.7821 (pm20) cc_final: 0.7296 (pm20) outliers start: 45 outliers final: 34 residues processed: 318 average time/residue: 0.2200 time to fit residues: 94.2687 Evaluate side-chains 320 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 282 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 425 VAL Chi-restraints excluded: chain L residue 124 VAL 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 A residue 425 VAL 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 D residue 436 MET Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 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 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 M residue 432 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 165 SER Chi-restraints excluded: chain O residue 265 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 95 optimal weight: 7.9990 chunk 72 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 68 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.122971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.107188 restraints weight = 14698.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.110236 restraints weight = 7422.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.112381 restraints weight = 4576.234| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4259 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= 0.304 Angle : 0.695 8.911 12365 Z= 0.353 Chirality : 0.048 0.163 1435 Planarity : 0.007 0.074 1555 Dihedral : 6.375 71.543 1292 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer: Outliers : 4.66 % Allowed : 27.83 % 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: -3.01 (0.23), residues: 1165 helix: -0.93 (0.29), residues: 330 sheet: -2.48 (0.46), residues: 120 loop : -2.56 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 268 HIS 0.009 0.001 HIS F 146 PHE 0.010 0.001 PHE C 208 TYR 0.018 0.002 TYR F 161 ARG 0.008 0.001 ARG D 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 325 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 281 time to evaluate : 0.996 Fit side-chains REVERT: J 412 ARG cc_start: 0.7548 (mtt180) cc_final: 0.6789 (mpp-170) REVERT: K 394 LYS cc_start: 0.9228 (ttmt) cc_final: 0.8864 (ttmm) REVERT: L 112 MET cc_start: 0.7598 (tpt) cc_final: 0.7116 (tpp) REVERT: L 186 THR cc_start: 0.9318 (t) cc_final: 0.9009 (m) REVERT: L 203 TYR cc_start: 0.9149 (t80) cc_final: 0.8705 (t80) REVERT: B 388 PHE cc_start: 0.8370 (m-10) cc_final: 0.8107 (m-80) REVERT: B 394 LYS cc_start: 0.9335 (ttmt) cc_final: 0.8994 (ttmm) REVERT: C 136 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8662 (tt) REVERT: C 168 ASP cc_start: 0.8826 (t70) cc_final: 0.8283 (t70) REVERT: C 189 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8750 (pttm) REVERT: C 265 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8315 (t) REVERT: E 394 LYS cc_start: 0.9288 (ttmt) cc_final: 0.8925 (ttmm) REVERT: E 411 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7264 (tp) REVERT: F 266 GLU cc_start: 0.7912 (pm20) cc_final: 0.7654 (pm20) REVERT: G 412 ARG cc_start: 0.7620 (mtt180) cc_final: 0.6889 (mpp-170) REVERT: H 386 TYR cc_start: 0.8904 (t80) cc_final: 0.8370 (t80) REVERT: H 394 LYS cc_start: 0.9350 (ttmt) cc_final: 0.8981 (ttmm) REVERT: I 112 MET cc_start: 0.7409 (tpt) cc_final: 0.7150 (tpp) REVERT: I 133 TYR cc_start: 0.8856 (m-80) cc_final: 0.8353 (m-80) REVERT: I 186 THR cc_start: 0.9546 (t) cc_final: 0.9343 (m) REVERT: I 204 SER cc_start: 0.9260 (t) cc_final: 0.8761 (p) REVERT: I 266 GLU cc_start: 0.7751 (pm20) cc_final: 0.7475 (pm20) REVERT: M 412 ARG cc_start: 0.7598 (mtt180) cc_final: 0.7009 (mpp-170) REVERT: N 394 LYS cc_start: 0.9287 (ttmt) cc_final: 0.9034 (ttmm) REVERT: O 114 MET cc_start: 0.7332 (pmt) cc_final: 0.7038 (pmt) REVERT: O 178 MET cc_start: 0.8742 (mtp) cc_final: 0.8405 (mtt) REVERT: O 266 GLU cc_start: 0.7856 (pm20) cc_final: 0.7382 (pm20) outliers start: 44 outliers final: 38 residues processed: 306 average time/residue: 0.2233 time to fit residues: 91.4189 Evaluate side-chains 321 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 279 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 124 VAL 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 A residue 425 VAL Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 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 F residue 258 THR Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain G residue 432 THR 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 137 VAL Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain M residue 425 VAL Chi-restraints excluded: chain M residue 432 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 265 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 202 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.121254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.105609 restraints weight = 14777.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.108466 restraints weight = 7443.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.110637 restraints weight = 4640.449| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9125 Z= 0.339 Angle : 0.722 10.301 12365 Z= 0.369 Chirality : 0.049 0.170 1435 Planarity : 0.007 0.076 1555 Dihedral : 6.485 69.818 1292 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 4.66 % Allowed : 28.25 % Favored : 67.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.23), residues: 1165 helix: -0.97 (0.29), residues: 330 sheet: -2.48 (0.46), residues: 120 loop : -2.58 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 196 HIS 0.009 0.001 HIS F 146 PHE 0.012 0.002 PHE O 208 TYR 0.018 0.002 TYR I 133 ARG 0.017 0.001 ARG J 437 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2924.61 seconds wall clock time: 53 minutes 44.96 seconds (3224.96 seconds total)