Starting phenix.real_space_refine on Wed Mar 4 08:23:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lig_23375/03_2026/7lig_23375.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lig_23375/03_2026/7lig_23375.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lig_23375/03_2026/7lig_23375.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lig_23375/03_2026/7lig_23375.map" model { file = "/net/cci-nas-00/data/ceres_data/7lig_23375/03_2026/7lig_23375.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lig_23375/03_2026/7lig_23375.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.050 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 120 5.16 5 C 8000 2.51 5 N 1940 2.21 5 O 2088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12148 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3023 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 9, 'TRANS': 371} Chain breaks: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'DE3': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 2.51, per 1000 atoms: 0.21 Number of scatterers: 12148 At special positions: 0 Unit cell: (114.33, 114.33, 92.7, 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 120 16.00 O 2088 8.00 N 1940 7.00 C 8000 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 548.3 milliseconds 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2928 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 82.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 12 through 31 removed outlier: 4.013A pdb=" N HIS A 16 " --> pdb=" O ASP A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 48 removed outlier: 3.657A pdb=" N LYS A 47 " --> pdb=" O ASN A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 75 removed outlier: 3.600A pdb=" N SER A 55 " --> pdb=" O ARG A 51 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS A 74 " --> pdb=" O CYS A 70 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 75 " --> pdb=" O ILE A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 105 removed outlier: 4.401A pdb=" N VAL A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN A 105 " --> pdb=" O SER A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 118 removed outlier: 3.956A pdb=" N LEU A 109 " --> pdb=" O ASN A 105 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 111 " --> pdb=" O ARG A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 161 removed outlier: 4.190A pdb=" N LYS A 129 " --> pdb=" O PRO A 125 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N MET A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N SER A 131 " --> pdb=" O GLY A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 167 removed outlier: 3.912A pdb=" N LEU A 166 " --> pdb=" O PRO A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 247 Proline residue: A 216 - end of helix removed outlier: 3.512A pdb=" N GLY A 247 " --> pdb=" O CYS A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 366 removed outlier: 4.280A pdb=" N SER A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N VAL A 341 " --> pdb=" O ILE A 337 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR A 342 " --> pdb=" O VAL A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 407 removed outlier: 3.672A pdb=" N LEU A 379 " --> pdb=" O PRO A 375 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 381 " --> pdb=" O MET A 377 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 removed outlier: 4.072A pdb=" N VAL A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 411 through 416' Processing helix chain 'A' and resid 418 through 433 removed outlier: 3.823A pdb=" N GLN A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 469 removed outlier: 3.586A pdb=" N ASN A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 31 Processing helix chain 'B' and resid 44 through 48 removed outlier: 3.658A pdb=" N LYS B 47 " --> pdb=" O ASN B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 75 removed outlier: 3.600A pdb=" N SER B 55 " --> pdb=" O ARG B 51 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 75 " --> pdb=" O ILE B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 105 removed outlier: 4.401A pdb=" N VAL B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN B 105 " --> pdb=" O SER B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 118 removed outlier: 3.957A pdb=" N LEU B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU B 110 " --> pdb=" O SER B 106 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 161 removed outlier: 4.190A pdb=" N LYS B 129 " --> pdb=" O PRO B 125 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N MET B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N SER B 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 167 removed outlier: 3.913A pdb=" N LEU B 166 " --> pdb=" O PRO B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 247 Proline residue: B 216 - end of helix removed outlier: 3.513A pdb=" N GLY B 247 " --> pdb=" O CYS B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 366 removed outlier: 4.278A pdb=" N SER B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL B 341 " --> pdb=" O ILE B 337 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR B 342 " --> pdb=" O VAL B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 407 removed outlier: 3.672A pdb=" N LEU B 379 " --> pdb=" O PRO B 375 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 381 " --> pdb=" O MET B 377 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 416 removed outlier: 4.071A pdb=" N VAL B 415 " --> pdb=" O SER B 411 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 416 " --> pdb=" O SER B 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 411 through 416' Processing helix chain 'B' and resid 418 through 433 removed outlier: 3.823A pdb=" N GLN B 426 " --> pdb=" O ARG B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 469 removed outlier: 3.587A pdb=" N ASN B 469 " --> pdb=" O LEU B 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 31 Processing helix chain 'C' and resid 44 through 48 removed outlier: 3.657A pdb=" N LYS C 47 " --> pdb=" O ASN C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 75 removed outlier: 3.600A pdb=" N SER C 55 " --> pdb=" O ARG C 51 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS C 74 " --> pdb=" O CYS C 70 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 75 " --> pdb=" O ILE C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 105 removed outlier: 4.401A pdb=" N VAL C 88 " --> pdb=" O ASN C 84 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN C 105 " --> pdb=" O SER C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 118 removed outlier: 3.956A pdb=" N LEU C 109 " --> pdb=" O ASN C 105 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU C 110 " --> pdb=" O SER C 106 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR C 111 " --> pdb=" O ARG C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 161 removed outlier: 4.190A pdb=" N LYS C 129 " --> pdb=" O PRO C 125 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N MET C 130 " --> pdb=" O ARG C 126 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N SER C 131 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 167 removed outlier: 3.913A pdb=" N LEU C 166 " --> pdb=" O PRO C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 247 Proline residue: C 216 - end of helix removed outlier: 3.513A pdb=" N GLY C 247 " --> pdb=" O CYS C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 366 removed outlier: 4.279A pdb=" N SER C 340 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL C 341 " --> pdb=" O ILE C 337 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR C 342 " --> pdb=" O VAL C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 407 removed outlier: 3.672A pdb=" N LEU C 379 " --> pdb=" O PRO C 375 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 381 " --> pdb=" O MET C 377 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL C 398 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 416 removed outlier: 4.072A pdb=" N VAL C 415 " --> pdb=" O SER C 411 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 411 through 416' Processing helix chain 'C' and resid 418 through 433 removed outlier: 3.823A pdb=" N GLN C 426 " --> pdb=" O ARG C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 469 removed outlier: 3.587A pdb=" N ASN C 469 " --> pdb=" O LEU C 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 31 Processing helix chain 'D' and resid 44 through 48 removed outlier: 3.657A pdb=" N LYS D 47 " --> pdb=" O ASN D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 75 removed outlier: 3.600A pdb=" N SER D 55 " --> pdb=" O ARG D 51 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 75 " --> pdb=" O ILE D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 105 removed outlier: 4.401A pdb=" N VAL D 88 " --> pdb=" O ASN D 84 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 118 removed outlier: 3.956A pdb=" N LEU D 109 " --> pdb=" O ASN D 105 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU D 110 " --> pdb=" O SER D 106 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 161 removed outlier: 4.189A pdb=" N LYS D 129 " --> pdb=" O PRO D 125 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N MET D 130 " --> pdb=" O ARG D 126 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N SER D 131 " --> pdb=" O GLY D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 167 removed outlier: 3.913A pdb=" N LEU D 166 " --> pdb=" O PRO D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 247 Proline residue: D 216 - end of helix removed outlier: 3.513A pdb=" N GLY D 247 " --> pdb=" O CYS D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 366 removed outlier: 4.279A pdb=" N SER D 340 " --> pdb=" O GLU D 336 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL D 341 " --> pdb=" O ILE D 337 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR D 342 " --> pdb=" O VAL D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 407 removed outlier: 3.671A pdb=" N LEU D 379 " --> pdb=" O PRO D 375 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU D 381 " --> pdb=" O MET D 377 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET D 382 " --> pdb=" O VAL D 378 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL D 398 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA D 399 " --> pdb=" O ALA D 395 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS D 407 " --> pdb=" O LEU D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 416 removed outlier: 4.072A pdb=" N VAL D 415 " --> pdb=" O SER D 411 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU D 416 " --> pdb=" O SER D 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 411 through 416' Processing helix chain 'D' and resid 418 through 433 removed outlier: 3.823A pdb=" N GLN D 426 " --> pdb=" O ARG D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 469 removed outlier: 3.587A pdb=" N ASN D 469 " --> pdb=" O LEU D 465 " (cutoff:3.500A) 928 hydrogen bonds defined for protein. 2772 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.71 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1780 1.31 - 1.43: 3527 1.43 - 1.56: 6941 1.56 - 1.68: 4 1.68 - 1.81: 172 Bond restraints: 12424 Sorted by residual: bond pdb=" CAH DE3 D 900 " pdb=" NAM DE3 D 900 " ideal model delta sigma weight residual 1.347 1.455 -0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" CAH DE3 C 900 " pdb=" NAM DE3 C 900 " ideal model delta sigma weight residual 1.347 1.455 -0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" CAH DE3 B 900 " pdb=" NAM DE3 B 900 " ideal model delta sigma weight residual 1.347 1.455 -0.108 2.00e-02 2.50e+03 2.89e+01 bond pdb=" CAH DE3 A 900 " pdb=" NAM DE3 A 900 " ideal model delta sigma weight residual 1.347 1.454 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" CAH DE3 C 900 " pdb=" OAN DE3 C 900 " ideal model delta sigma weight residual 1.226 1.180 0.046 2.00e-02 2.50e+03 5.25e+00 ... (remaining 12419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 15917 1.60 - 3.20: 800 3.20 - 4.81: 103 4.81 - 6.41: 24 6.41 - 8.01: 8 Bond angle restraints: 16852 Sorted by residual: angle pdb=" N ALA C 215 " pdb=" CA ALA C 215 " pdb=" C ALA C 215 " ideal model delta sigma weight residual 112.17 116.04 -3.87 1.36e+00 5.41e-01 8.09e+00 angle pdb=" N ALA A 215 " pdb=" CA ALA A 215 " pdb=" C ALA A 215 " ideal model delta sigma weight residual 112.17 116.01 -3.84 1.36e+00 5.41e-01 7.99e+00 angle pdb=" N ALA D 215 " pdb=" CA ALA D 215 " pdb=" C ALA D 215 " ideal model delta sigma weight residual 112.17 116.00 -3.83 1.36e+00 5.41e-01 7.94e+00 angle pdb=" N ALA B 215 " pdb=" CA ALA B 215 " pdb=" C ALA B 215 " ideal model delta sigma weight residual 112.17 115.97 -3.80 1.36e+00 5.41e-01 7.81e+00 angle pdb=" C SER B 370 " pdb=" N PHE B 371 " pdb=" CA PHE B 371 " ideal model delta sigma weight residual 121.54 126.75 -5.21 1.91e+00 2.74e-01 7.44e+00 ... (remaining 16847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 6404 17.90 - 35.79: 676 35.79 - 53.69: 152 53.69 - 71.58: 32 71.58 - 89.48: 16 Dihedral angle restraints: 7280 sinusoidal: 2772 harmonic: 4508 Sorted by residual: dihedral pdb=" CA ALA A 365 " pdb=" C ALA A 365 " pdb=" N ALA A 366 " pdb=" CA ALA A 366 " ideal model delta harmonic sigma weight residual -180.00 -163.00 -17.00 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ALA C 365 " pdb=" C ALA C 365 " pdb=" N ALA C 366 " pdb=" CA ALA C 366 " ideal model delta harmonic sigma weight residual -180.00 -163.00 -17.00 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ALA D 365 " pdb=" C ALA D 365 " pdb=" N ALA D 366 " pdb=" CA ALA D 366 " ideal model delta harmonic sigma weight residual -180.00 -163.02 -16.98 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 7277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1125 0.030 - 0.059: 554 0.059 - 0.089: 219 0.089 - 0.118: 80 0.118 - 0.148: 38 Chirality restraints: 2016 Sorted by residual: chirality pdb=" CG LEU C 349 " pdb=" CB LEU C 349 " pdb=" CD1 LEU C 349 " pdb=" CD2 LEU C 349 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CG LEU D 349 " pdb=" CB LEU D 349 " pdb=" CD1 LEU D 349 " pdb=" CD2 LEU D 349 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CG LEU B 349 " pdb=" CB LEU B 349 " pdb=" CD1 LEU B 349 " pdb=" CD2 LEU B 349 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 2013 not shown) Planarity restraints: 2020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 195 " 0.053 5.00e-02 4.00e+02 7.89e-02 9.96e+00 pdb=" N PRO D 196 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO D 196 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 196 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 195 " 0.052 5.00e-02 4.00e+02 7.87e-02 9.91e+00 pdb=" N PRO A 196 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 196 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 196 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 195 " -0.052 5.00e-02 4.00e+02 7.87e-02 9.90e+00 pdb=" N PRO B 196 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 196 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 196 " -0.044 5.00e-02 4.00e+02 ... (remaining 2017 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 3999 2.84 - 3.36: 12257 3.36 - 3.87: 19632 3.87 - 4.39: 21455 4.39 - 4.90: 37560 Nonbonded interactions: 94903 Sorted by model distance: nonbonded pdb=" O ILE A 210 " pdb=" OG1 THR A 214 " model vdw 2.328 3.040 nonbonded pdb=" O ILE D 210 " pdb=" OG1 THR D 214 " model vdw 2.328 3.040 nonbonded pdb=" O ILE B 210 " pdb=" OG1 THR B 214 " model vdw 2.329 3.040 nonbonded pdb=" O ILE C 210 " pdb=" OG1 THR C 214 " model vdw 2.329 3.040 nonbonded pdb=" O SER D 31 " pdb=" OG SER D 31 " model vdw 2.331 3.040 ... (remaining 94898 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.570 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 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 : 0.006 0.108 12424 Z= 0.280 Angle : 0.801 8.010 16852 Z= 0.468 Chirality : 0.044 0.148 2016 Planarity : 0.008 0.079 2020 Dihedral : 16.002 89.477 4352 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.47 % Allowed : 7.96 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.19), residues: 1500 helix: -0.74 (0.13), residues: 1160 sheet: None (None), residues: 0 loop : -1.91 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 18 TYR 0.014 0.002 TYR A 380 PHE 0.023 0.002 PHE A 363 TRP 0.009 0.002 TRP B 20 HIS 0.003 0.001 HIS A 33 Details of bonding type rmsd covalent geometry : bond 0.00572 (12424) covalent geometry : angle 0.80075 (16852) hydrogen bonds : bond 0.13252 ( 928) hydrogen bonds : angle 5.34200 ( 2772) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 248 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 377 MET cc_start: 0.8284 (mtt) cc_final: 0.8051 (mtt) REVERT: C 353 SER cc_start: 0.8154 (OUTLIER) cc_final: 0.7912 (m) REVERT: C 377 MET cc_start: 0.8390 (mtt) cc_final: 0.7883 (mtt) REVERT: D 377 MET cc_start: 0.8326 (mtt) cc_final: 0.8062 (mtt) outliers start: 20 outliers final: 4 residues processed: 267 average time/residue: 0.4397 time to fit residues: 130.2840 Evaluate side-chains 153 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 148 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 363 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.0010 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 447 ASN B 114 ASN C 94 GLN C 114 ASN D 94 GLN D 114 ASN D 447 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.123919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.096923 restraints weight = 20492.728| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 3.36 r_work: 0.3228 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12424 Z= 0.144 Angle : 0.523 6.475 16852 Z= 0.280 Chirality : 0.036 0.135 2016 Planarity : 0.005 0.061 2020 Dihedral : 5.040 55.606 1662 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.02 % Allowed : 17.92 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.22), residues: 1500 helix: 1.27 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -1.02 (0.39), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 373 TYR 0.022 0.001 TYR B 204 PHE 0.024 0.001 PHE B 183 TRP 0.011 0.001 TRP D 20 HIS 0.005 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00272 (12424) covalent geometry : angle 0.52271 (16852) hydrogen bonds : bond 0.06168 ( 928) hydrogen bonds : angle 3.89541 ( 2772) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 0.497 Fit side-chains REVERT: A 227 MET cc_start: 0.8105 (mmp) cc_final: 0.7888 (mmp) REVERT: A 239 MET cc_start: 0.7629 (ttm) cc_final: 0.7351 (ttm) REVERT: A 377 MET cc_start: 0.7663 (mtt) cc_final: 0.6817 (mtm) REVERT: B 83 LEU cc_start: 0.7335 (mt) cc_final: 0.7080 (mt) REVERT: B 239 MET cc_start: 0.7498 (ttm) cc_final: 0.7225 (ttm) REVERT: B 377 MET cc_start: 0.7965 (mtt) cc_final: 0.7175 (mtm) REVERT: C 227 MET cc_start: 0.8154 (mmp) cc_final: 0.7909 (mmp) REVERT: C 454 MET cc_start: 0.7240 (ttt) cc_final: 0.6964 (ttt) REVERT: C 458 MET cc_start: 0.6571 (tmt) cc_final: 0.6223 (mtm) REVERT: D 227 MET cc_start: 0.8072 (mmp) cc_final: 0.7860 (mmp) outliers start: 41 outliers final: 7 residues processed: 182 average time/residue: 0.4063 time to fit residues: 83.0768 Evaluate side-chains 151 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 144 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain D residue 363 PHE Chi-restraints excluded: chain D residue 468 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 147 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 140 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 HIS A 52 GLN B 45 GLN B 114 ASN B 447 ASN C 16 HIS C 114 ASN D 16 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.122489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.095513 restraints weight = 20949.080| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 3.41 r_work: 0.3234 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12424 Z= 0.148 Angle : 0.508 6.617 16852 Z= 0.269 Chirality : 0.037 0.141 2016 Planarity : 0.004 0.049 2020 Dihedral : 4.479 39.379 1656 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.70 % Allowed : 20.94 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.22), residues: 1500 helix: 1.82 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -0.85 (0.38), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 18 TYR 0.018 0.001 TYR A 204 PHE 0.010 0.001 PHE D 350 TRP 0.011 0.002 TRP D 187 HIS 0.007 0.001 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00304 (12424) covalent geometry : angle 0.50814 (16852) hydrogen bonds : bond 0.06009 ( 928) hydrogen bonds : angle 3.81830 ( 2772) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.530 Fit side-chains REVERT: A 227 MET cc_start: 0.8139 (mmp) cc_final: 0.7882 (mmp) REVERT: A 239 MET cc_start: 0.7593 (ttm) cc_final: 0.7294 (ttm) REVERT: A 377 MET cc_start: 0.7618 (mtt) cc_final: 0.6746 (mtm) REVERT: B 34 TRP cc_start: 0.8302 (t-100) cc_final: 0.7955 (t-100) REVERT: B 227 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7611 (tpp) REVERT: B 239 MET cc_start: 0.7506 (ttm) cc_final: 0.7217 (ttm) REVERT: B 363 PHE cc_start: 0.7898 (OUTLIER) cc_final: 0.7694 (m-80) REVERT: C 34 TRP cc_start: 0.8160 (t-100) cc_final: 0.7889 (t-100) REVERT: C 227 MET cc_start: 0.8138 (mmp) cc_final: 0.7896 (mmp) REVERT: C 454 MET cc_start: 0.7347 (ttt) cc_final: 0.7100 (ttt) REVERT: C 458 MET cc_start: 0.6414 (tmt) cc_final: 0.6108 (mtm) REVERT: D 182 ARG cc_start: 0.8968 (mtm-85) cc_final: 0.8222 (ptp90) outliers start: 23 outliers final: 7 residues processed: 177 average time/residue: 0.4410 time to fit residues: 87.2192 Evaluate side-chains 149 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 140 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 PHE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 363 PHE Chi-restraints excluded: chain D residue 468 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 56 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 86 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 116 optimal weight: 0.2980 chunk 142 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN B 16 HIS B 94 GLN B 114 ASN C 94 GLN D 94 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.124619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.097640 restraints weight = 20288.857| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 3.37 r_work: 0.3246 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12424 Z= 0.142 Angle : 0.507 6.975 16852 Z= 0.266 Chirality : 0.037 0.186 2016 Planarity : 0.004 0.040 2020 Dihedral : 4.388 39.501 1656 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.58 % Allowed : 21.83 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.22), residues: 1500 helix: 2.10 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -0.69 (0.39), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 373 TYR 0.016 0.001 TYR A 204 PHE 0.009 0.001 PHE A 350 TRP 0.008 0.001 TRP B 20 HIS 0.006 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00290 (12424) covalent geometry : angle 0.50745 (16852) hydrogen bonds : bond 0.05741 ( 928) hydrogen bonds : angle 3.75473 ( 2772) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 0.508 Fit side-chains REVERT: A 190 PHE cc_start: 0.7191 (OUTLIER) cc_final: 0.6823 (m-80) REVERT: A 239 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.7206 (ttm) REVERT: A 377 MET cc_start: 0.7652 (mtt) cc_final: 0.6943 (mtm) REVERT: B 34 TRP cc_start: 0.8287 (t-100) cc_final: 0.8034 (t-100) REVERT: B 239 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.7058 (ttm) REVERT: C 34 TRP cc_start: 0.8204 (t-100) cc_final: 0.7876 (t-100) REVERT: C 227 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7922 (mmp) REVERT: C 454 MET cc_start: 0.7353 (ttt) cc_final: 0.7119 (ttt) REVERT: C 458 MET cc_start: 0.6502 (tmt) cc_final: 0.6202 (mtm) REVERT: D 182 ARG cc_start: 0.8930 (mtm-85) cc_final: 0.7622 (ptp-170) outliers start: 35 outliers final: 8 residues processed: 177 average time/residue: 0.4232 time to fit residues: 83.9094 Evaluate side-chains 154 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 363 PHE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 363 PHE Chi-restraints excluded: chain D residue 468 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 41 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 57 optimal weight: 0.0270 chunk 134 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 ASN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 ASN D 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.124737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.097379 restraints weight = 20905.568| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.37 r_work: 0.3257 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12424 Z= 0.138 Angle : 0.510 8.062 16852 Z= 0.266 Chirality : 0.037 0.176 2016 Planarity : 0.004 0.034 2020 Dihedral : 4.345 39.286 1656 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.62 % Allowed : 23.82 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.23), residues: 1500 helix: 2.25 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -0.55 (0.40), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 18 TYR 0.015 0.001 TYR C 128 PHE 0.007 0.001 PHE D 350 TRP 0.008 0.001 TRP B 155 HIS 0.006 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00283 (12424) covalent geometry : angle 0.51018 (16852) hydrogen bonds : bond 0.05642 ( 928) hydrogen bonds : angle 3.73363 ( 2772) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.488 Fit side-chains REVERT: A 190 PHE cc_start: 0.7127 (m-80) cc_final: 0.6839 (m-80) REVERT: A 239 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.7233 (ttm) REVERT: A 454 MET cc_start: 0.7699 (ttm) cc_final: 0.7466 (ttt) REVERT: B 34 TRP cc_start: 0.8239 (t-100) cc_final: 0.8008 (t-100) REVERT: B 239 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.7095 (ttm) REVERT: B 377 MET cc_start: 0.7295 (mtm) cc_final: 0.6856 (mtm) REVERT: C 34 TRP cc_start: 0.8258 (t-100) cc_final: 0.7940 (t-100) REVERT: C 227 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7796 (mmp) REVERT: C 454 MET cc_start: 0.7371 (ttt) cc_final: 0.7146 (ttt) REVERT: C 458 MET cc_start: 0.6404 (tmt) cc_final: 0.6147 (mtm) outliers start: 22 outliers final: 4 residues processed: 165 average time/residue: 0.4288 time to fit residues: 79.3306 Evaluate side-chains 142 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 135 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 363 PHE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain D residue 363 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 93 optimal weight: 0.1980 chunk 31 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 126 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN B 114 ASN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN C 469 ASN D 469 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.125011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.097357 restraints weight = 20953.356| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 3.40 r_work: 0.3256 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12424 Z= 0.138 Angle : 0.526 9.903 16852 Z= 0.273 Chirality : 0.037 0.173 2016 Planarity : 0.003 0.033 2020 Dihedral : 4.346 39.417 1656 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.06 % Allowed : 23.60 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.23), residues: 1500 helix: 2.31 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -0.48 (0.40), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 387 TYR 0.016 0.001 TYR C 128 PHE 0.008 0.001 PHE B 363 TRP 0.009 0.001 TRP B 155 HIS 0.007 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00285 (12424) covalent geometry : angle 0.52644 (16852) hydrogen bonds : bond 0.05539 ( 928) hydrogen bonds : angle 3.71840 ( 2772) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.519 Fit side-chains REVERT: A 227 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7833 (mmp) REVERT: A 239 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.7245 (ttm) REVERT: A 377 MET cc_start: 0.7109 (mtm) cc_final: 0.6371 (mtm) REVERT: C 34 TRP cc_start: 0.8249 (t-100) cc_final: 0.8027 (t-100) REVERT: C 227 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7793 (mmp) REVERT: C 239 MET cc_start: 0.7942 (ttm) cc_final: 0.7678 (ttp) REVERT: C 407 HIS cc_start: 0.7745 (OUTLIER) cc_final: 0.7528 (t-90) REVERT: D 182 ARG cc_start: 0.8897 (mtm-85) cc_final: 0.7650 (ptp-170) REVERT: D 227 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7882 (mmp) REVERT: D 239 MET cc_start: 0.7855 (ttm) cc_final: 0.7603 (ttp) outliers start: 28 outliers final: 5 residues processed: 170 average time/residue: 0.4560 time to fit residues: 86.3623 Evaluate side-chains 147 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 363 PHE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 407 HIS Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 363 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 8.9990 chunk 147 optimal weight: 0.9980 chunk 120 optimal weight: 0.0270 chunk 74 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 91 optimal weight: 0.0040 chunk 118 optimal weight: 0.0870 chunk 55 optimal weight: 6.9990 overall best weight: 0.3428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN B 114 ASN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.127271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.100055 restraints weight = 20629.146| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 3.39 r_work: 0.3302 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12424 Z= 0.127 Angle : 0.548 12.907 16852 Z= 0.280 Chirality : 0.036 0.178 2016 Planarity : 0.003 0.035 2020 Dihedral : 4.347 38.302 1656 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.55 % Allowed : 24.93 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.22), residues: 1500 helix: 2.39 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -0.42 (0.40), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 373 TYR 0.022 0.001 TYR C 128 PHE 0.015 0.001 PHE C 363 TRP 0.022 0.001 TRP A 187 HIS 0.008 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00249 (12424) covalent geometry : angle 0.54820 (16852) hydrogen bonds : bond 0.05113 ( 928) hydrogen bonds : angle 3.62403 ( 2772) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.591 Fit side-chains REVERT: A 336 GLU cc_start: 0.8777 (tt0) cc_final: 0.8451 (tt0) REVERT: A 377 MET cc_start: 0.6930 (mtm) cc_final: 0.6429 (mtm) REVERT: B 182 ARG cc_start: 0.8883 (mtm-85) cc_final: 0.8062 (ptp90) REVERT: B 239 MET cc_start: 0.7473 (ttm) cc_final: 0.7199 (ttm) REVERT: B 377 MET cc_start: 0.7223 (mtm) cc_final: 0.6668 (mtm) REVERT: C 227 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7319 (mpp) REVERT: C 239 MET cc_start: 0.7845 (ttm) cc_final: 0.7602 (ttp) REVERT: D 182 ARG cc_start: 0.8929 (mtm-85) cc_final: 0.7690 (ptp-170) REVERT: D 239 MET cc_start: 0.7850 (ttm) cc_final: 0.7613 (ttp) REVERT: D 336 GLU cc_start: 0.8758 (tt0) cc_final: 0.8457 (tt0) outliers start: 21 outliers final: 6 residues processed: 181 average time/residue: 0.4309 time to fit residues: 86.8892 Evaluate side-chains 162 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 155 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain D residue 24 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 45 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 151 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 93 optimal weight: 0.4980 chunk 67 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 ASN ** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.124956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.097245 restraints weight = 20991.650| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 3.41 r_work: 0.3254 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12424 Z= 0.149 Angle : 0.563 11.450 16852 Z= 0.288 Chirality : 0.037 0.166 2016 Planarity : 0.003 0.033 2020 Dihedral : 4.322 39.964 1656 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.18 % Allowed : 25.88 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.74 (0.22), residues: 1500 helix: 2.39 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -0.41 (0.39), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 373 TYR 0.028 0.001 TYR C 128 PHE 0.009 0.001 PHE B 450 TRP 0.020 0.002 TRP B 187 HIS 0.007 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00325 (12424) covalent geometry : angle 0.56261 (16852) hydrogen bonds : bond 0.05535 ( 928) hydrogen bonds : angle 3.68377 ( 2772) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.463 Fit side-chains REVERT: A 197 MET cc_start: 0.7336 (ppp) cc_final: 0.7048 (ppp) REVERT: A 336 GLU cc_start: 0.8778 (tt0) cc_final: 0.8492 (tt0) REVERT: A 377 MET cc_start: 0.6917 (mtm) cc_final: 0.6465 (mtm) REVERT: B 182 ARG cc_start: 0.8852 (mtm-85) cc_final: 0.7984 (ptp90) REVERT: B 377 MET cc_start: 0.7163 (mtm) cc_final: 0.6618 (mtm) REVERT: B 458 MET cc_start: 0.6937 (OUTLIER) cc_final: 0.6287 (tmm) REVERT: C 227 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7240 (mpp) REVERT: C 239 MET cc_start: 0.7882 (ttm) cc_final: 0.7652 (ttp) REVERT: C 458 MET cc_start: 0.6887 (tmm) cc_final: 0.6458 (mtp) REVERT: D 182 ARG cc_start: 0.8799 (mtm-85) cc_final: 0.7668 (ptp90) REVERT: D 239 MET cc_start: 0.7837 (ttm) cc_final: 0.7622 (ttp) REVERT: D 336 GLU cc_start: 0.8785 (tt0) cc_final: 0.8500 (tt0) REVERT: D 377 MET cc_start: 0.7252 (mtm) cc_final: 0.6772 (mtm) outliers start: 16 outliers final: 6 residues processed: 170 average time/residue: 0.4738 time to fit residues: 89.2255 Evaluate side-chains 157 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain D residue 24 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 91 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 chunk 147 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 150 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.126320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.098085 restraints weight = 20274.995| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 3.41 r_work: 0.3243 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12424 Z= 0.148 Angle : 0.573 10.174 16852 Z= 0.294 Chirality : 0.037 0.164 2016 Planarity : 0.003 0.032 2020 Dihedral : 4.362 40.870 1656 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.40 % Allowed : 26.25 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.76 (0.22), residues: 1500 helix: 2.39 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -0.37 (0.40), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 373 TYR 0.035 0.001 TYR C 128 PHE 0.018 0.001 PHE D 363 TRP 0.018 0.002 TRP B 187 HIS 0.007 0.001 HIS B 233 Details of bonding type rmsd covalent geometry : bond 0.00319 (12424) covalent geometry : angle 0.57252 (16852) hydrogen bonds : bond 0.05539 ( 928) hydrogen bonds : angle 3.69060 ( 2772) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.321 Fit side-chains REVERT: A 336 GLU cc_start: 0.8803 (tt0) cc_final: 0.8502 (tt0) REVERT: B 182 ARG cc_start: 0.8799 (mtm-85) cc_final: 0.7971 (ptp90) REVERT: B 377 MET cc_start: 0.7122 (mtm) cc_final: 0.6623 (mtm) REVERT: B 458 MET cc_start: 0.7183 (OUTLIER) cc_final: 0.6478 (tmm) REVERT: C 227 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7288 (mpp) REVERT: C 239 MET cc_start: 0.7892 (ttm) cc_final: 0.7671 (ttp) REVERT: C 458 MET cc_start: 0.6907 (tmm) cc_final: 0.6553 (mtt) REVERT: D 336 GLU cc_start: 0.8777 (tt0) cc_final: 0.8499 (tt0) REVERT: D 377 MET cc_start: 0.7120 (mtm) cc_final: 0.6704 (mtm) outliers start: 19 outliers final: 8 residues processed: 165 average time/residue: 0.4813 time to fit residues: 88.4187 Evaluate side-chains 157 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 184 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 0 optimal weight: 8.9990 chunk 135 optimal weight: 0.5980 chunk 150 optimal weight: 0.7980 chunk 51 optimal weight: 0.4980 chunk 11 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 129 optimal weight: 0.5980 chunk 143 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 ASN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.126001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.097623 restraints weight = 20471.918| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 3.43 r_work: 0.3250 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12424 Z= 0.147 Angle : 0.593 14.797 16852 Z= 0.302 Chirality : 0.038 0.178 2016 Planarity : 0.003 0.032 2020 Dihedral : 4.359 40.411 1656 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.96 % Allowed : 26.92 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.22), residues: 1500 helix: 2.38 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -0.40 (0.40), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 373 TYR 0.045 0.002 TYR C 128 PHE 0.021 0.001 PHE A 363 TRP 0.016 0.002 TRP B 187 HIS 0.007 0.001 HIS A 233 Details of bonding type rmsd covalent geometry : bond 0.00316 (12424) covalent geometry : angle 0.59327 (16852) hydrogen bonds : bond 0.05530 ( 928) hydrogen bonds : angle 3.69105 ( 2772) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.606 Fit side-chains REVERT: A 336 GLU cc_start: 0.8813 (tt0) cc_final: 0.8511 (tt0) REVERT: A 377 MET cc_start: 0.6832 (mtm) cc_final: 0.6120 (mtm) REVERT: B 377 MET cc_start: 0.6961 (mtm) cc_final: 0.6559 (mtm) REVERT: B 458 MET cc_start: 0.7146 (OUTLIER) cc_final: 0.6447 (tmm) REVERT: C 227 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7285 (mpp) REVERT: C 239 MET cc_start: 0.7949 (ttm) cc_final: 0.7695 (ttp) REVERT: C 336 GLU cc_start: 0.8702 (tt0) cc_final: 0.8477 (tt0) REVERT: C 372 THR cc_start: 0.9017 (p) cc_final: 0.8711 (t) REVERT: C 377 MET cc_start: 0.7134 (mtm) cc_final: 0.6586 (mtm) REVERT: C 458 MET cc_start: 0.6907 (tmm) cc_final: 0.6460 (mtp) REVERT: D 233 HIS cc_start: 0.7865 (t70) cc_final: 0.7658 (t70) REVERT: D 336 GLU cc_start: 0.8776 (tt0) cc_final: 0.8504 (tt0) REVERT: D 377 MET cc_start: 0.6970 (mtm) cc_final: 0.6590 (mtm) outliers start: 13 outliers final: 7 residues processed: 158 average time/residue: 0.4716 time to fit residues: 82.8401 Evaluate side-chains 156 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain D residue 184 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 110 optimal weight: 0.4980 chunk 84 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 ASN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.125290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.096865 restraints weight = 20352.348| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.43 r_work: 0.3240 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12424 Z= 0.155 Angle : 0.596 9.310 16852 Z= 0.305 Chirality : 0.038 0.176 2016 Planarity : 0.003 0.031 2020 Dihedral : 4.376 41.593 1656 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.81 % Allowed : 27.06 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.22), residues: 1500 helix: 2.33 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -0.40 (0.40), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 373 TYR 0.042 0.002 TYR C 128 PHE 0.017 0.001 PHE D 363 TRP 0.014 0.002 TRP B 187 HIS 0.007 0.001 HIS D 233 Details of bonding type rmsd covalent geometry : bond 0.00341 (12424) covalent geometry : angle 0.59584 (16852) hydrogen bonds : bond 0.05698 ( 928) hydrogen bonds : angle 3.72986 ( 2772) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3334.96 seconds wall clock time: 57 minutes 58.99 seconds (3478.99 seconds total)