Starting phenix.real_space_refine on Wed Jul 30 07:51:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lig_23375/07_2025/7lig_23375.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lig_23375/07_2025/7lig_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_23375/07_2025/7lig_23375.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lig_23375/07_2025/7lig_23375.map" model { file = "/net/cci-nas-00/data/ceres_data/7lig_23375/07_2025/7lig_23375.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lig_23375/07_2025/7lig_23375.cif" } resolution = 2.9 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= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: C, B, D Time building chain proxies: 7.25, per 1000 atoms: 0.60 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: 3.20 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 1.26 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: 5.15 Time building geometry restraints manager: 3.45 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 133.490 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: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 35.280 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 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:22.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 192.380 ------------------------------------------------------------------------------- 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 (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: -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 TRP 0.009 0.002 TRP B 20 HIS 0.003 0.001 HIS A 33 PHE 0.023 0.002 PHE A 363 TYR 0.014 0.002 TYR A 380 ARG 0.003 0.000 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.13252 ( 928) hydrogen bonds : angle 5.34200 ( 2772) covalent geometry : bond 0.00572 (12424) covalent geometry : angle 0.80075 (16852) *********************** 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 : 2.630 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: 0.9305 time to fit residues: 278.5494 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 : 1.313 ------------------------------------------------------------------------------- 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 128 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 ASN D 447 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.121981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.094998 restraints weight = 20528.499| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 3.34 r_work: 0.3195 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.1861 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= 0.160 Angle : 0.538 6.180 16852 Z= 0.288 Chirality : 0.037 0.135 2016 Planarity : 0.005 0.062 2020 Dihedral : 5.089 55.261 1662 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.32 % Allowed : 18.29 % Favored : 78.39 % 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: 1.03 (0.22), residues: 1500 helix: 1.18 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -1.02 (0.40), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 20 HIS 0.006 0.001 HIS A 233 PHE 0.024 0.001 PHE B 183 TYR 0.021 0.002 TYR B 204 ARG 0.002 0.000 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.06599 ( 928) hydrogen bonds : angle 3.98095 ( 2772) covalent geometry : bond 0.00325 (12424) covalent geometry : angle 0.53789 (16852) *********************** 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 194 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 149 time to evaluate : 1.410 Fit side-chains REVERT: A 34 TRP cc_start: 0.8240 (t-100) cc_final: 0.7964 (t-100) REVERT: A 239 MET cc_start: 0.7708 (ttm) cc_final: 0.7423 (ttm) REVERT: A 377 MET cc_start: 0.7663 (mtt) cc_final: 0.6808 (mtm) REVERT: B 83 LEU cc_start: 0.7470 (mt) cc_final: 0.7203 (mt) REVERT: B 212 LEU cc_start: 0.8138 (mt) cc_final: 0.7522 (tt) REVERT: B 227 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7491 (mpp) REVERT: B 239 MET cc_start: 0.7553 (ttm) cc_final: 0.7280 (ttm) REVERT: B 377 MET cc_start: 0.7862 (mtt) cc_final: 0.7064 (mtm) REVERT: C 227 MET cc_start: 0.8182 (mmp) cc_final: 0.7962 (mmp) REVERT: C 454 MET cc_start: 0.7309 (ttt) cc_final: 0.7066 (ttt) REVERT: C 458 MET cc_start: 0.6554 (tmt) cc_final: 0.6195 (mtm) REVERT: D 377 MET cc_start: 0.7993 (mtt) cc_final: 0.7101 (mtm) outliers start: 45 outliers final: 14 residues processed: 171 average time/residue: 0.9171 time to fit residues: 176.1286 Evaluate side-chains 151 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 100 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 150 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 135 optimal weight: 0.6980 chunk 149 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 45 GLN B 114 ASN B 447 ASN C 16 HIS D 16 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.121311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.094266 restraints weight = 21170.754| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.40 r_work: 0.3217 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12424 Z= 0.153 Angle : 0.519 6.594 16852 Z= 0.275 Chirality : 0.037 0.133 2016 Planarity : 0.004 0.052 2020 Dihedral : 4.516 39.574 1656 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.77 % Allowed : 21.53 % Favored : 76.70 % 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: 1.82 (0.22), residues: 1500 helix: 1.77 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -0.86 (0.39), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 187 HIS 0.007 0.001 HIS B 46 PHE 0.009 0.001 PHE D 350 TYR 0.018 0.001 TYR B 204 ARG 0.002 0.000 ARG A 18 Details of bonding type rmsd hydrogen bonds : bond 0.06189 ( 928) hydrogen bonds : angle 3.87450 ( 2772) covalent geometry : bond 0.00321 (12424) covalent geometry : angle 0.51908 (16852) *********************** 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 181 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 1.325 Fit side-chains REVERT: A 34 TRP cc_start: 0.8230 (t-100) cc_final: 0.7962 (t-100) REVERT: A 239 MET cc_start: 0.7596 (ttm) cc_final: 0.7299 (ttm) REVERT: A 377 MET cc_start: 0.7695 (mtt) cc_final: 0.6801 (mtm) REVERT: B 34 TRP cc_start: 0.8295 (t-100) cc_final: 0.7980 (t-100) REVERT: B 227 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7510 (mpp) REVERT: B 239 MET cc_start: 0.7509 (ttm) cc_final: 0.7209 (ttm) REVERT: C 34 TRP cc_start: 0.8174 (t-100) cc_final: 0.7806 (t-100) REVERT: C 227 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7919 (mmp) REVERT: C 454 MET cc_start: 0.7396 (ttt) cc_final: 0.7157 (ttt) REVERT: C 458 MET cc_start: 0.6424 (tmt) cc_final: 0.6112 (mtm) REVERT: D 207 VAL cc_start: 0.6923 (m) cc_final: 0.6703 (m) REVERT: D 377 MET cc_start: 0.7927 (mtt) cc_final: 0.7044 (mtm) outliers start: 24 outliers final: 8 residues processed: 173 average time/residue: 0.8458 time to fit residues: 164.2656 Evaluate side-chains 148 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 1.299 ------------------------------------------------------------------------------- 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 468 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.6980 chunk 134 optimal weight: 0.6980 chunk 123 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 17 optimal weight: 0.2980 chunk 73 optimal weight: 0.0970 chunk 23 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 HIS B 16 HIS B 94 GLN C 94 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.124747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.097962 restraints weight = 20416.521| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 3.32 r_work: 0.3276 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.2643 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= 0.133 Angle : 0.510 7.258 16852 Z= 0.265 Chirality : 0.037 0.191 2016 Planarity : 0.004 0.043 2020 Dihedral : 4.408 37.993 1656 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.29 % Allowed : 22.57 % Favored : 75.15 % 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: 2.37 (0.23), residues: 1500 helix: 2.14 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -0.61 (0.39), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 155 HIS 0.006 0.001 HIS B 233 PHE 0.010 0.001 PHE A 350 TYR 0.016 0.001 TYR B 204 ARG 0.002 0.000 ARG B 387 Details of bonding type rmsd hydrogen bonds : bond 0.05540 ( 928) hydrogen bonds : angle 3.72636 ( 2772) covalent geometry : bond 0.00261 (12424) covalent geometry : angle 0.51037 (16852) *********************** 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 190 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 2.189 Fit side-chains REVERT: A 239 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.7222 (ttm) REVERT: B 34 TRP cc_start: 0.8276 (t-100) cc_final: 0.8031 (t-100) REVERT: B 212 LEU cc_start: 0.8267 (mt) cc_final: 0.8055 (mt) REVERT: B 239 MET cc_start: 0.7385 (ttm) cc_final: 0.7075 (ttm) REVERT: C 34 TRP cc_start: 0.8203 (t-100) cc_final: 0.7927 (t-100) REVERT: C 227 MET cc_start: 0.8077 (mmp) cc_final: 0.7773 (mmp) REVERT: C 454 MET cc_start: 0.7295 (ttt) cc_final: 0.7031 (ttt) REVERT: C 458 MET cc_start: 0.6422 (tmt) cc_final: 0.6202 (mtm) REVERT: D 182 ARG cc_start: 0.9044 (mtm-85) cc_final: 0.8224 (ptp90) REVERT: D 227 MET cc_start: 0.7988 (mmp) cc_final: 0.7757 (mmp) outliers start: 31 outliers final: 9 residues processed: 176 average time/residue: 1.0880 time to fit residues: 214.4505 Evaluate side-chains 154 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE 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 C residue 24 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 103 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 20 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 129 optimal weight: 0.0470 chunk 16 optimal weight: 7.9990 chunk 9 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 GLN C 469 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.126363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.098902 restraints weight = 20604.113| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 3.39 r_work: 0.3285 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.2894 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= 0.130 Angle : 0.500 7.524 16852 Z= 0.260 Chirality : 0.037 0.170 2016 Planarity : 0.004 0.037 2020 Dihedral : 4.317 38.349 1656 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.55 % Allowed : 23.38 % Favored : 75.07 % 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: 2.58 (0.23), residues: 1500 helix: 2.29 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -0.55 (0.39), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 155 HIS 0.005 0.001 HIS B 233 PHE 0.009 0.001 PHE B 363 TYR 0.018 0.001 TYR C 128 ARG 0.002 0.000 ARG A 18 Details of bonding type rmsd hydrogen bonds : bond 0.05401 ( 928) hydrogen bonds : angle 3.71033 ( 2772) covalent geometry : bond 0.00255 (12424) covalent geometry : angle 0.49956 (16852) *********************** 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 176 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 1.259 Fit side-chains REVERT: A 239 MET cc_start: 0.7538 (ttm) cc_final: 0.7251 (ttm) REVERT: A 377 MET cc_start: 0.7232 (mtm) cc_final: 0.6577 (mtm) REVERT: B 239 MET cc_start: 0.7357 (OUTLIER) cc_final: 0.7056 (ttm) REVERT: B 349 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.6290 (tt) REVERT: C 227 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7810 (mmp) REVERT: C 454 MET cc_start: 0.7256 (ttt) cc_final: 0.6994 (ttt) REVERT: C 458 MET cc_start: 0.6425 (tmt) cc_final: 0.6216 (mtm) REVERT: D 182 ARG cc_start: 0.8952 (mtm-85) cc_final: 0.7684 (ptp-170) REVERT: D 227 MET cc_start: 0.8080 (mmp) cc_final: 0.7877 (mmp) REVERT: D 239 MET cc_start: 0.8010 (ttm) cc_final: 0.7769 (ttp) REVERT: D 377 MET cc_start: 0.7220 (mtm) cc_final: 0.6594 (mtm) outliers start: 21 outliers final: 4 residues processed: 169 average time/residue: 0.9105 time to fit residues: 172.3313 Evaluate side-chains 147 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 140 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 PHE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 463 ILE 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 118 optimal weight: 0.0030 chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 0.0170 chunk 42 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 6 optimal weight: 0.0060 chunk 56 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 overall best weight: 0.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.126902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.099886 restraints weight = 20933.358| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 3.42 r_work: 0.3303 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12424 Z= 0.124 Angle : 0.515 9.820 16852 Z= 0.264 Chirality : 0.036 0.171 2016 Planarity : 0.003 0.035 2020 Dihedral : 4.298 38.128 1656 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.92 % Allowed : 24.12 % Favored : 73.97 % 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: 2.69 (0.23), residues: 1500 helix: 2.36 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -0.49 (0.39), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 34 HIS 0.007 0.001 HIS B 233 PHE 0.013 0.001 PHE C 363 TYR 0.016 0.001 TYR C 128 ARG 0.001 0.000 ARG B 373 Details of bonding type rmsd hydrogen bonds : bond 0.05143 ( 928) hydrogen bonds : angle 3.64599 ( 2772) covalent geometry : bond 0.00239 (12424) covalent geometry : angle 0.51451 (16852) *********************** 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 193 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 1.407 Fit side-chains REVERT: A 377 MET cc_start: 0.7095 (mtm) cc_final: 0.6541 (mtm) REVERT: B 227 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7732 (tpp) REVERT: B 239 MET cc_start: 0.7338 (OUTLIER) cc_final: 0.7032 (ttm) REVERT: C 239 MET cc_start: 0.7780 (ttm) cc_final: 0.7570 (ttp) REVERT: C 454 MET cc_start: 0.7220 (ttt) cc_final: 0.6943 (ttt) REVERT: D 182 ARG cc_start: 0.8959 (mtm-85) cc_final: 0.7707 (ptp-170) REVERT: D 227 MET cc_start: 0.8034 (mmp) cc_final: 0.7740 (mmp) REVERT: D 336 GLU cc_start: 0.8710 (tt0) cc_final: 0.8336 (tt0) outliers start: 26 outliers final: 4 residues processed: 185 average time/residue: 0.9163 time to fit residues: 190.1900 Evaluate side-chains 159 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 153 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 PHE Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 24 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 149 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 GLN B 114 ASN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.124151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.096493 restraints weight = 20996.979| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 3.39 r_work: 0.3244 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12424 Z= 0.155 Angle : 0.550 8.364 16852 Z= 0.286 Chirality : 0.038 0.169 2016 Planarity : 0.004 0.034 2020 Dihedral : 4.316 40.317 1656 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.33 % Allowed : 25.52 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.22), residues: 1500 helix: 2.27 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -0.40 (0.40), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 187 HIS 0.007 0.001 HIS A 233 PHE 0.016 0.001 PHE D 363 TYR 0.020 0.001 TYR B 99 ARG 0.002 0.000 ARG D 373 Details of bonding type rmsd hydrogen bonds : bond 0.05674 ( 928) hydrogen bonds : angle 3.74556 ( 2772) covalent geometry : bond 0.00341 (12424) covalent geometry : angle 0.54997 (16852) *********************** 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 168 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 2.293 Fit side-chains REVERT: A 190 PHE cc_start: 0.7295 (OUTLIER) cc_final: 0.7035 (m-80) REVERT: A 336 GLU cc_start: 0.8781 (tt0) cc_final: 0.8473 (tt0) REVERT: B 227 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7776 (tpp) REVERT: B 377 MET cc_start: 0.7203 (mtm) cc_final: 0.6613 (mtm) REVERT: B 458 MET cc_start: 0.6785 (mtm) cc_final: 0.6432 (tmm) REVERT: D 227 MET cc_start: 0.8080 (mmp) cc_final: 0.7783 (mmp) REVERT: D 239 MET cc_start: 0.7986 (ttm) cc_final: 0.7699 (ttp) REVERT: D 336 GLU cc_start: 0.8766 (tt0) cc_final: 0.8487 (tt0) REVERT: D 377 MET cc_start: 0.7298 (mtm) cc_final: 0.6577 (mtm) REVERT: D 407 HIS cc_start: 0.7786 (OUTLIER) cc_final: 0.6990 (m-70) outliers start: 18 outliers final: 8 residues processed: 165 average time/residue: 1.2227 time to fit residues: 226.1479 Evaluate side-chains 154 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 190 PHE 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 227 MET Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 407 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 132 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.124680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.096717 restraints weight = 21080.324| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 3.41 r_work: 0.3246 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.3204 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= 0.148 Angle : 0.550 10.201 16852 Z= 0.284 Chirality : 0.037 0.162 2016 Planarity : 0.003 0.034 2020 Dihedral : 4.348 40.940 1656 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.96 % Allowed : 26.62 % Favored : 72.42 % 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: 2.66 (0.23), residues: 1500 helix: 2.32 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -0.44 (0.40), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 187 HIS 0.007 0.001 HIS B 233 PHE 0.010 0.001 PHE C 363 TYR 0.024 0.001 TYR C 128 ARG 0.002 0.000 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.05622 ( 928) hydrogen bonds : angle 3.73134 ( 2772) covalent geometry : bond 0.00320 (12424) covalent geometry : angle 0.54980 (16852) *********************** 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 164 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 1.322 Fit side-chains REVERT: A 336 GLU cc_start: 0.8755 (tt0) cc_final: 0.8464 (tt0) REVERT: A 377 MET cc_start: 0.7164 (mtm) cc_final: 0.6470 (mtm) REVERT: B 227 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7776 (tpp) REVERT: B 377 MET cc_start: 0.7146 (mtm) cc_final: 0.6611 (mtm) REVERT: C 239 MET cc_start: 0.7992 (ttm) cc_final: 0.7732 (ttp) REVERT: C 372 THR cc_start: 0.9063 (p) cc_final: 0.8769 (t) REVERT: C 458 MET cc_start: 0.7080 (OUTLIER) cc_final: 0.6473 (tmm) REVERT: D 227 MET cc_start: 0.8129 (mmp) cc_final: 0.7858 (mmp) REVERT: D 239 MET cc_start: 0.7978 (ttm) cc_final: 0.7720 (ttp) REVERT: D 336 GLU cc_start: 0.8738 (tt0) cc_final: 0.8436 (tt0) REVERT: D 377 MET cc_start: 0.7146 (mtm) cc_final: 0.6535 (mtm) REVERT: D 407 HIS cc_start: 0.7795 (OUTLIER) cc_final: 0.7032 (m-70) outliers start: 13 outliers final: 9 residues processed: 161 average time/residue: 0.9093 time to fit residues: 164.2922 Evaluate side-chains 152 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 1.450 ------------------------------------------------------------------------------- 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 227 MET Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 407 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 110 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 46 HIS ** 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 = 0.3798 r_free = 0.3798 target = 0.124516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.096754 restraints weight = 20811.364| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 3.38 r_work: 0.3251 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12424 Z= 0.149 Angle : 0.556 8.417 16852 Z= 0.288 Chirality : 0.038 0.165 2016 Planarity : 0.003 0.033 2020 Dihedral : 4.355 40.780 1656 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.18 % Allowed : 26.33 % Favored : 72.49 % 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: 2.69 (0.22), residues: 1500 helix: 2.34 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -0.42 (0.40), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 187 HIS 0.007 0.001 HIS B 233 PHE 0.012 0.001 PHE D 363 TYR 0.030 0.001 TYR C 128 ARG 0.002 0.000 ARG D 373 Details of bonding type rmsd hydrogen bonds : bond 0.05648 ( 928) hydrogen bonds : angle 3.74162 ( 2772) covalent geometry : bond 0.00321 (12424) covalent geometry : angle 0.55605 (16852) *********************** 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 164 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 1.387 Fit side-chains REVERT: A 336 GLU cc_start: 0.8763 (tt0) cc_final: 0.8385 (tt0) REVERT: A 377 MET cc_start: 0.6986 (mtm) cc_final: 0.6359 (mtm) REVERT: B 182 ARG cc_start: 0.8843 (mtm-85) cc_final: 0.8115 (ptp90) REVERT: B 227 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7822 (tpp) REVERT: B 377 MET cc_start: 0.7111 (mtm) cc_final: 0.6595 (mtm) REVERT: B 407 HIS cc_start: 0.7824 (OUTLIER) cc_final: 0.7563 (t-90) REVERT: B 458 MET cc_start: 0.6801 (mtm) cc_final: 0.6389 (tmm) REVERT: C 239 MET cc_start: 0.7969 (ttm) cc_final: 0.7746 (ttp) REVERT: C 372 THR cc_start: 0.9043 (p) cc_final: 0.8762 (t) REVERT: C 458 MET cc_start: 0.7149 (OUTLIER) cc_final: 0.6421 (tmm) REVERT: D 227 MET cc_start: 0.8116 (mmp) cc_final: 0.7841 (mmp) REVERT: D 239 MET cc_start: 0.7986 (ttm) cc_final: 0.7745 (ttp) REVERT: D 336 GLU cc_start: 0.8792 (tt0) cc_final: 0.8501 (tt0) REVERT: D 377 MET cc_start: 0.7130 (mtm) cc_final: 0.6536 (mtm) REVERT: D 407 HIS cc_start: 0.7802 (OUTLIER) cc_final: 0.7541 (t-90) outliers start: 16 outliers final: 9 residues processed: 160 average time/residue: 0.9259 time to fit residues: 165.6429 Evaluate side-chains 155 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 1.364 ------------------------------------------------------------------------------- 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 227 MET Chi-restraints excluded: chain B residue 407 HIS Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 407 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 8.9990 chunk 135 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 55 optimal weight: 0.0060 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 46 HIS ** 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 = 0.3812 r_free = 0.3812 target = 0.125569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.097687 restraints weight = 20768.050| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 3.38 r_work: 0.3263 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12424 Z= 0.143 Angle : 0.564 11.191 16852 Z= 0.291 Chirality : 0.038 0.170 2016 Planarity : 0.003 0.029 2020 Dihedral : 4.351 40.709 1656 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.03 % Allowed : 26.62 % 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 (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: 2.78 (0.22), residues: 1500 helix: 2.41 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -0.40 (0.40), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 187 HIS 0.010 0.001 HIS B 233 PHE 0.016 0.001 PHE A 363 TYR 0.038 0.002 TYR C 128 ARG 0.003 0.000 ARG C 373 Details of bonding type rmsd hydrogen bonds : bond 0.05527 ( 928) hydrogen bonds : angle 3.72633 ( 2772) covalent geometry : bond 0.00304 (12424) covalent geometry : angle 0.56401 (16852) ********************** 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: 14 poor density : 151 time to evaluate : 1.464 Fit side-chains REVERT: A 233 HIS cc_start: 0.7812 (t70) cc_final: 0.7595 (t70) REVERT: A 336 GLU cc_start: 0.8767 (tt0) cc_final: 0.8450 (tt0) REVERT: A 377 MET cc_start: 0.6868 (mtm) cc_final: 0.6270 (mtm) REVERT: B 227 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7805 (tpp) REVERT: B 377 MET cc_start: 0.6884 (mtm) cc_final: 0.6433 (mtm) REVERT: B 407 HIS cc_start: 0.7802 (OUTLIER) cc_final: 0.7558 (t-90) REVERT: C 190 PHE cc_start: 0.7595 (OUTLIER) cc_final: 0.7366 (m-80) REVERT: C 239 MET cc_start: 0.7935 (ttm) cc_final: 0.7701 (ttp) REVERT: C 372 THR cc_start: 0.9035 (p) cc_final: 0.8751 (t) REVERT: C 377 MET cc_start: 0.7006 (mtm) cc_final: 0.6574 (mtm) REVERT: C 458 MET cc_start: 0.7050 (OUTLIER) cc_final: 0.6500 (tmt) REVERT: D 227 MET cc_start: 0.8112 (mmp) cc_final: 0.7821 (mmp) REVERT: D 239 MET cc_start: 0.7956 (ttm) cc_final: 0.7727 (ttp) REVERT: D 336 GLU cc_start: 0.8794 (tt0) cc_final: 0.8521 (tt0) REVERT: D 407 HIS cc_start: 0.7786 (OUTLIER) cc_final: 0.7531 (t-90) outliers start: 14 outliers final: 8 residues processed: 163 average time/residue: 0.9027 time to fit residues: 165.0254 Evaluate side-chains 153 residues out of total 1356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 1.302 ------------------------------------------------------------------------------- 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 227 MET Chi-restraints excluded: chain B residue 407 HIS Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 458 MET Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 407 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 84 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 94 optimal weight: 0.0980 chunk 7 optimal weight: 0.9980 chunk 82 optimal weight: 0.0020 chunk 124 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 46 HIS ** 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 = 0.3831 r_free = 0.3831 target = 0.127114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.099223 restraints weight = 20797.457| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 3.42 r_work: 0.3284 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12424 Z= 0.135 Angle : 0.561 10.585 16852 Z= 0.289 Chirality : 0.038 0.186 2016 Planarity : 0.003 0.029 2020 Dihedral : 4.350 39.930 1656 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.74 % Allowed : 26.99 % Favored : 72.27 % 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: 2.82 (0.22), residues: 1500 helix: 2.44 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -0.40 (0.40), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 187 HIS 0.007 0.001 HIS B 233 PHE 0.009 0.001 PHE D 363 TYR 0.038 0.002 TYR C 128 ARG 0.002 0.000 ARG D 373 Details of bonding type rmsd hydrogen bonds : bond 0.05311 ( 928) hydrogen bonds : angle 3.70346 ( 2772) covalent geometry : bond 0.00277 (12424) covalent geometry : angle 0.56112 (16852) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7682.26 seconds wall clock time: 136 minutes 28.89 seconds (8188.89 seconds total)