Starting phenix.real_space_refine on Tue Mar 3 21:26:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jyi_22526/03_2026/7jyi_22526.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jyi_22526/03_2026/7jyi_22526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jyi_22526/03_2026/7jyi_22526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jyi_22526/03_2026/7jyi_22526.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jyi_22526/03_2026/7jyi_22526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jyi_22526/03_2026/7jyi_22526.map" } resolution = 3.4 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= 0.000 sd= 0.012 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 62 5.16 5 C 5586 2.51 5 N 1512 2.21 5 O 1647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 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: 8807 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 3799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3799 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 16, 'TRANS': 484} Chain: "D" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 604 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 3799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3799 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 16, 'TRANS': 484} Chain: "F" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 605 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 2.24, per 1000 atoms: 0.25 Number of scatterers: 8807 At special positions: 0 Unit cell: (104.5, 158.4, 81.4, 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 62 16.00 O 1647 8.00 N 1512 7.00 C 5586 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 30 " distance=2.29 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 121 " distance=2.03 Simple disulfide: pdb=" SG CYS E 3 " - pdb=" SG CYS E 30 " distance=2.29 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 121 " distance=2.03 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: 0.67 Conformation dependent library (CDL) restraints added in 303.9 milliseconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 24 sheets defined 26.6% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.931A pdb=" N SER C 86 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 152 removed outlier: 3.556A pdb=" N ILE C 152 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 200 removed outlier: 3.535A pdb=" N ASP C 200 " --> pdb=" O ASP C 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 197 through 200' Processing helix chain 'C' and resid 214 through 219 Processing helix chain 'C' and resid 238 through 241 removed outlier: 3.765A pdb=" N ALA C 241 " --> pdb=" O ASN C 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 238 through 241' Processing helix chain 'C' and resid 261 through 270 removed outlier: 3.521A pdb=" N ALA C 268 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA C 270 " --> pdb=" O HIS C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 425 Processing helix chain 'C' and resid 426 through 431 removed outlier: 4.008A pdb=" N PHE C 431 " --> pdb=" O ALA C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 455 Processing helix chain 'C' and resid 461 through 478 Processing helix chain 'C' and resid 484 through 496 removed outlier: 3.914A pdb=" N LEU C 491 " --> pdb=" O THR C 487 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL C 494 " --> pdb=" O ALA C 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 25 removed outlier: 4.264A pdb=" N TYR D 25 " --> pdb=" O SER D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 39 removed outlier: 3.628A pdb=" N LYS D 31 " --> pdb=" O LYS D 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 54 removed outlier: 3.905A pdb=" N LEU D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 71 removed outlier: 3.874A pdb=" N LYS D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL D 61 " --> pdb=" O THR D 57 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'E' and resid 82 through 86 removed outlier: 3.931A pdb=" N SER E 86 " --> pdb=" O ASP E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 152 removed outlier: 3.556A pdb=" N ILE E 152 " --> pdb=" O SER E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 200 removed outlier: 3.535A pdb=" N ASP E 200 " --> pdb=" O ASP E 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 197 through 200' Processing helix chain 'E' and resid 214 through 219 Processing helix chain 'E' and resid 238 through 241 removed outlier: 3.765A pdb=" N ALA E 241 " --> pdb=" O ASN E 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 238 through 241' Processing helix chain 'E' and resid 261 through 270 removed outlier: 3.520A pdb=" N ALA E 268 " --> pdb=" O ALA E 264 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA E 270 " --> pdb=" O HIS E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 425 Processing helix chain 'E' and resid 426 through 431 removed outlier: 4.008A pdb=" N PHE E 431 " --> pdb=" O ALA E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 455 Processing helix chain 'E' and resid 461 through 478 Processing helix chain 'E' and resid 484 through 496 removed outlier: 3.914A pdb=" N LEU E 491 " --> pdb=" O THR E 487 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL E 494 " --> pdb=" O ALA E 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 39 Processing helix chain 'F' and resid 41 through 54 removed outlier: 3.750A pdb=" N VAL F 45 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU F 52 " --> pdb=" O ALA F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 71 Processing sheet with id=AA1, first strand: chain 'C' and resid 9 through 13 removed outlier: 6.559A pdb=" N ASP C 10 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N MET C 34 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL C 12 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ARG C 138 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N THR C 48 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU C 136 " --> pdb=" O THR C 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 9 through 13 removed outlier: 6.559A pdb=" N ASP C 10 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N MET C 34 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL C 12 " --> pdb=" O MET C 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 20 through 23 removed outlier: 3.663A pdb=" N ARG C 292 " --> pdb=" O ASP C 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 90 through 95 removed outlier: 8.966A pdb=" N LEU C 113 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N SER C 70 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N THR C 115 " --> pdb=" O MET C 68 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N MET C 68 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ALA C 117 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N SER C 66 " --> pdb=" O ALA C 117 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N PHE C 119 " --> pdb=" O SER C 64 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N SER C 64 " --> pdb=" O PHE C 119 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N CYS C 121 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N GLU C 62 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS C 123 " --> pdb=" O CYS C 60 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N CYS C 60 " --> pdb=" O LYS C 123 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N MET C 125 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER C 58 " --> pdb=" O MET C 125 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLY C 127 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA C 54 " --> pdb=" O SER C 129 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER C 58 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 90 through 95 removed outlier: 4.279A pdb=" N HIS C 210 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU C 273 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 98 through 99 Processing sheet with id=AA7, first strand: chain 'C' and resid 243 through 247 Processing sheet with id=AA8, first strand: chain 'C' and resid 319 through 320 removed outlier: 3.641A pdb=" N ALA C 319 " --> pdb=" O THR C 327 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 329 through 333 removed outlier: 3.580A pdb=" N SER C 372 " --> pdb=" O TYR C 332 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 339 through 340 Processing sheet with id=AB2, first strand: chain 'C' and resid 343 through 346 Processing sheet with id=AB3, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.752A pdb=" N ARG C 357 " --> pdb=" O ASP C 379 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 9 through 13 removed outlier: 6.558A pdb=" N ASP E 10 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N MET E 34 " --> pdb=" O ASP E 10 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL E 12 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ARG E 138 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N THR E 48 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU E 136 " --> pdb=" O THR E 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 9 through 13 removed outlier: 6.558A pdb=" N ASP E 10 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N MET E 34 " --> pdb=" O ASP E 10 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL E 12 " --> pdb=" O MET E 34 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 20 through 23 removed outlier: 3.663A pdb=" N ARG E 292 " --> pdb=" O ASP E 189 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 90 through 95 removed outlier: 8.966A pdb=" N LEU E 113 " --> pdb=" O SER E 70 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N SER E 70 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N THR E 115 " --> pdb=" O MET E 68 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N MET E 68 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ALA E 117 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N SER E 66 " --> pdb=" O ALA E 117 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N PHE E 119 " --> pdb=" O SER E 64 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N SER E 64 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N CYS E 121 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU E 62 " --> pdb=" O CYS E 121 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS E 123 " --> pdb=" O CYS E 60 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N CYS E 60 " --> pdb=" O LYS E 123 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N MET E 125 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER E 58 " --> pdb=" O MET E 125 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLY E 127 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA E 54 " --> pdb=" O SER E 129 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER E 58 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 90 through 95 removed outlier: 4.279A pdb=" N HIS E 210 " --> pdb=" O ALA E 275 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU E 273 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 98 through 99 Processing sheet with id=AC1, first strand: chain 'E' and resid 243 through 247 Processing sheet with id=AC2, first strand: chain 'E' and resid 319 through 320 removed outlier: 3.642A pdb=" N ALA E 319 " --> pdb=" O THR E 327 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 329 through 333 removed outlier: 3.581A pdb=" N SER E 372 " --> pdb=" O TYR E 332 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 339 through 340 Processing sheet with id=AC5, first strand: chain 'E' and resid 343 through 346 Processing sheet with id=AC6, first strand: chain 'E' and resid 357 through 358 removed outlier: 3.752A pdb=" N ARG E 357 " --> pdb=" O ASP E 379 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 918 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: 1.24 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2851 1.34 - 1.46: 1666 1.46 - 1.57: 4384 1.57 - 1.69: 0 1.69 - 1.80: 98 Bond restraints: 8999 Sorted by residual: bond pdb=" CA TYR F 74 " pdb=" C TYR F 74 " ideal model delta sigma weight residual 1.532 1.516 0.016 9.60e-03 1.09e+04 2.77e+00 bond pdb=" CA THR E 479 " pdb=" CB THR E 479 " ideal model delta sigma weight residual 1.530 1.553 -0.023 1.51e-02 4.39e+03 2.31e+00 bond pdb=" CA THR C 479 " pdb=" CB THR C 479 " ideal model delta sigma weight residual 1.532 1.553 -0.021 1.48e-02 4.57e+03 2.07e+00 bond pdb=" CB VAL C 265 " pdb=" CG1 VAL C 265 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.83e+00 bond pdb=" CB VAL E 265 " pdb=" CG1 VAL E 265 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.80e+00 ... (remaining 8994 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 11899 1.96 - 3.91: 262 3.91 - 5.87: 27 5.87 - 7.82: 2 7.82 - 9.78: 6 Bond angle restraints: 12196 Sorted by residual: angle pdb=" C LEU E 498 " pdb=" N SER E 499 " pdb=" CA SER E 499 " ideal model delta sigma weight residual 121.54 131.32 -9.78 1.91e+00 2.74e-01 2.62e+01 angle pdb=" C LEU C 498 " pdb=" N SER C 499 " pdb=" CA SER C 499 " ideal model delta sigma weight residual 121.54 131.30 -9.76 1.91e+00 2.74e-01 2.61e+01 angle pdb=" CA THR E 479 " pdb=" CB THR E 479 " pdb=" CG2 THR E 479 " ideal model delta sigma weight residual 110.50 118.42 -7.92 1.70e+00 3.46e-01 2.17e+01 angle pdb=" CA THR C 479 " pdb=" CB THR C 479 " pdb=" CG2 THR C 479 " ideal model delta sigma weight residual 110.50 118.40 -7.90 1.70e+00 3.46e-01 2.16e+01 angle pdb=" CA HIS C 249 " pdb=" C HIS C 249 " pdb=" N ALA C 250 " ideal model delta sigma weight residual 119.71 115.25 4.46 1.17e+00 7.31e-01 1.45e+01 ... (remaining 12191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4712 17.98 - 35.96: 409 35.96 - 53.94: 132 53.94 - 71.92: 35 71.92 - 89.90: 9 Dihedral angle restraints: 5297 sinusoidal: 2045 harmonic: 3252 Sorted by residual: dihedral pdb=" CA LEU E 498 " pdb=" C LEU E 498 " pdb=" N SER E 499 " pdb=" CA SER E 499 " ideal model delta harmonic sigma weight residual -180.00 -142.62 -37.38 0 5.00e+00 4.00e-02 5.59e+01 dihedral pdb=" CA LEU C 498 " pdb=" C LEU C 498 " pdb=" N SER C 499 " pdb=" CA SER C 499 " ideal model delta harmonic sigma weight residual 180.00 -142.67 -37.33 0 5.00e+00 4.00e-02 5.57e+01 dihedral pdb=" CA HIS E 226 " pdb=" C HIS E 226 " pdb=" N ALA E 227 " pdb=" CA ALA E 227 " ideal model delta harmonic sigma weight residual -180.00 -152.62 -27.38 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 5294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1064 0.050 - 0.100: 265 0.100 - 0.150: 57 0.150 - 0.200: 0 0.200 - 0.250: 2 Chirality restraints: 1388 Sorted by residual: chirality pdb=" CB THR C 479 " pdb=" CA THR C 479 " pdb=" OG1 THR C 479 " pdb=" CG2 THR C 479 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB THR E 479 " pdb=" CA THR E 479 " pdb=" OG1 THR E 479 " pdb=" CG2 THR E 479 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA PRO C 132 " pdb=" N PRO C 132 " pdb=" C PRO C 132 " pdb=" CB PRO C 132 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 1385 not shown) Planarity restraints: 1537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 498 " 0.017 2.00e-02 2.50e+03 3.50e-02 1.23e+01 pdb=" C LEU C 498 " -0.061 2.00e-02 2.50e+03 pdb=" O LEU C 498 " 0.023 2.00e-02 2.50e+03 pdb=" N SER C 499 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 498 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C LEU E 498 " 0.060 2.00e-02 2.50e+03 pdb=" O LEU E 498 " -0.023 2.00e-02 2.50e+03 pdb=" N SER E 499 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 2 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.32e+00 pdb=" C ARG C 2 " -0.032 2.00e-02 2.50e+03 pdb=" O ARG C 2 " 0.012 2.00e-02 2.50e+03 pdb=" N CYS C 3 " 0.011 2.00e-02 2.50e+03 ... (remaining 1534 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 232 2.66 - 3.22: 7960 3.22 - 3.78: 12621 3.78 - 4.34: 17677 4.34 - 4.90: 30892 Nonbonded interactions: 69382 Sorted by model distance: nonbonded pdb=" OE2 GLU C 133 " pdb=" NH2 ARG C 193 " model vdw 2.104 3.120 nonbonded pdb=" OE2 GLU E 133 " pdb=" NH2 ARG E 193 " model vdw 2.104 3.120 nonbonded pdb=" O CYS E 488 " pdb=" CG LEU E 491 " model vdw 2.144 3.470 nonbonded pdb=" O CYS C 488 " pdb=" CG LEU C 491 " model vdw 2.146 3.470 nonbonded pdb=" O GLY E 436 " pdb=" OG SER E 440 " model vdw 2.179 3.040 ... (remaining 69377 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = (chain 'F' and (resid 1 through 74 or (resid 75 and (name N or name CA or name C \ or name O or name CB or name OG )))) } 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: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.240 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 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 : 0.009 0.260 9003 Z= 0.392 Angle : 0.745 9.778 12204 Z= 0.428 Chirality : 0.046 0.250 1388 Planarity : 0.004 0.035 1537 Dihedral : 16.050 89.897 3209 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.52 % Allowed : 10.31 % Favored : 89.16 % Rotamer: Outliers : 5.45 % Allowed : 16.14 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -4.54 (0.20), residues: 1144 helix: -1.77 (0.27), residues: 256 sheet: -2.54 (0.25), residues: 356 loop : -4.03 (0.20), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 94 TYR 0.027 0.002 TYR E 158 PHE 0.024 0.002 PHE E 431 TRP 0.012 0.001 TRP E 400 HIS 0.005 0.001 HIS C 226 Details of bonding type rmsd covalent geometry : bond 0.00783 ( 8999) covalent geometry : angle 0.74517 (12196) SS BOND : bond 0.18394 ( 4) SS BOND : angle 0.69929 ( 8) hydrogen bonds : bond 0.19434 ( 311) hydrogen bonds : angle 9.01216 ( 918) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 232 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: C 220 ASP cc_start: 0.7954 (m-30) cc_final: 0.7626 (m-30) REVERT: C 277 MET cc_start: 0.7956 (ttm) cc_final: 0.7604 (ttm) REVERT: C 295 MET cc_start: 0.8285 (ttm) cc_final: 0.7965 (mtp) REVERT: C 332 TYR cc_start: 0.7768 (t80) cc_final: 0.7544 (t80) REVERT: C 400 TRP cc_start: 0.8215 (t-100) cc_final: 0.7470 (t-100) REVERT: C 416 ARG cc_start: 0.7554 (ttm-80) cc_final: 0.7275 (mtm110) REVERT: C 449 PHE cc_start: 0.6486 (t80) cc_final: 0.5981 (m-10) REVERT: C 454 LYS cc_start: 0.8777 (ttpp) cc_final: 0.8197 (tmmt) REVERT: D 4 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8723 (mm) REVERT: E 4 ILE cc_start: 0.7977 (tt) cc_final: 0.7756 (mt) REVERT: E 151 MET cc_start: 0.5453 (mmt) cc_final: 0.5241 (mmp) REVERT: E 189 ASP cc_start: 0.7807 (t0) cc_final: 0.7586 (t70) REVERT: F 10 ARG cc_start: 0.9092 (mmt-90) cc_final: 0.8839 (mmt90) outliers start: 52 outliers final: 23 residues processed: 274 average time/residue: 0.0940 time to fit residues: 34.7629 Evaluate side-chains 183 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain F residue 56 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 147 GLN C 208 ASN C 219 HIS C 253 GLN C 362 ASN D 39 ASN E 85 GLN E 134 ASN E 147 GLN E 208 ASN E 219 HIS E 371 ASN E 439 ASN E 478 ASN ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.134471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.103236 restraints weight = 10398.321| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.08 r_work: 0.2875 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9003 Z= 0.165 Angle : 0.617 9.786 12204 Z= 0.315 Chirality : 0.043 0.171 1388 Planarity : 0.004 0.039 1537 Dihedral : 7.110 73.915 1252 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 5.03 % Allowed : 17.51 % Favored : 77.46 % 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: -3.53 (0.22), residues: 1144 helix: -0.70 (0.31), residues: 266 sheet: -2.10 (0.25), residues: 370 loop : -3.45 (0.22), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 402 TYR 0.010 0.001 TYR D 74 PHE 0.015 0.001 PHE C 431 TRP 0.011 0.001 TRP E 462 HIS 0.007 0.001 HIS C 226 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 8999) covalent geometry : angle 0.61595 (12196) SS BOND : bond 0.00620 ( 4) SS BOND : angle 1.57701 ( 8) hydrogen bonds : bond 0.03597 ( 311) hydrogen bonds : angle 5.72057 ( 918) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 180 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: C 71 ASP cc_start: 0.8605 (t70) cc_final: 0.8322 (t0) REVERT: C 189 ASP cc_start: 0.8051 (t0) cc_final: 0.7750 (t0) REVERT: C 332 TYR cc_start: 0.8257 (t80) cc_final: 0.7852 (t80) REVERT: C 400 TRP cc_start: 0.8368 (t-100) cc_final: 0.8119 (t-100) REVERT: C 416 ARG cc_start: 0.7863 (ttm-80) cc_final: 0.7350 (mtm110) REVERT: C 449 PHE cc_start: 0.6189 (t80) cc_final: 0.5196 (m-10) REVERT: C 454 LYS cc_start: 0.8681 (ttpp) cc_final: 0.8476 (ttpp) REVERT: C 477 LEU cc_start: 0.8659 (mt) cc_final: 0.8369 (mt) REVERT: D 4 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8562 (mm) REVERT: D 23 ARG cc_start: 0.8949 (ttm170) cc_final: 0.8564 (mtm-85) REVERT: E 74 CYS cc_start: 0.8243 (m) cc_final: 0.8011 (m) REVERT: E 189 ASP cc_start: 0.8439 (t0) cc_final: 0.8175 (t70) REVERT: E 377 GLU cc_start: 0.8787 (tt0) cc_final: 0.8583 (tt0) REVERT: E 454 LYS cc_start: 0.8568 (ttpp) cc_final: 0.8361 (tttm) outliers start: 48 outliers final: 27 residues processed: 214 average time/residue: 0.0893 time to fit residues: 26.3751 Evaluate side-chains 184 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 58 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 72 optimal weight: 30.0000 chunk 32 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 0.1980 chunk 21 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 439 ASN E 478 ASN ** F 7 HIS ** 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 = 0.3424 r_free = 0.3424 target = 0.135268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.105311 restraints weight = 10290.365| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.93 r_work: 0.2924 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9003 Z= 0.114 Angle : 0.554 7.737 12204 Z= 0.282 Chirality : 0.041 0.150 1388 Planarity : 0.004 0.041 1537 Dihedral : 5.751 73.327 1231 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 4.40 % Allowed : 18.76 % Favored : 76.83 % 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: -3.02 (0.23), residues: 1144 helix: -0.16 (0.33), residues: 264 sheet: -1.66 (0.26), residues: 350 loop : -3.27 (0.22), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 2 TYR 0.010 0.001 TYR D 74 PHE 0.011 0.001 PHE C 431 TRP 0.008 0.001 TRP C 20 HIS 0.007 0.001 HIS C 226 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8999) covalent geometry : angle 0.55366 (12196) SS BOND : bond 0.00346 ( 4) SS BOND : angle 0.75310 ( 8) hydrogen bonds : bond 0.03166 ( 311) hydrogen bonds : angle 5.05546 ( 918) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 171 time to evaluate : 0.267 Fit side-chains REVERT: C 15 MET cc_start: 0.6848 (OUTLIER) cc_final: 0.6592 (ptp) REVERT: C 73 ARG cc_start: 0.8261 (mmt180) cc_final: 0.7817 (mmm-85) REVERT: C 149 SER cc_start: 0.8102 (OUTLIER) cc_final: 0.7803 (m) REVERT: C 189 ASP cc_start: 0.7862 (t0) cc_final: 0.7596 (t0) REVERT: C 332 TYR cc_start: 0.8306 (t80) cc_final: 0.7962 (t80) REVERT: C 349 MET cc_start: 0.4949 (ttm) cc_final: 0.4427 (tmm) REVERT: C 416 ARG cc_start: 0.7639 (ttm-80) cc_final: 0.7193 (mtm110) REVERT: C 449 PHE cc_start: 0.6280 (t80) cc_final: 0.5199 (m-10) REVERT: C 456 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8162 (mp) REVERT: C 477 LEU cc_start: 0.8756 (mt) cc_final: 0.8400 (mt) REVERT: D 4 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8384 (mm) REVERT: D 23 ARG cc_start: 0.8956 (ttm170) cc_final: 0.8591 (mtm-85) REVERT: E 66 SER cc_start: 0.8966 (m) cc_final: 0.8470 (t) REVERT: E 92 CYS cc_start: 0.8808 (p) cc_final: 0.8459 (m) REVERT: E 151 MET cc_start: 0.5220 (mmt) cc_final: 0.4860 (mpp) REVERT: E 189 ASP cc_start: 0.8329 (t0) cc_final: 0.7943 (t70) REVERT: E 454 LYS cc_start: 0.8448 (ttpp) cc_final: 0.8223 (tttm) REVERT: F 10 ARG cc_start: 0.9075 (mmt90) cc_final: 0.8686 (mmm160) outliers start: 42 outliers final: 31 residues processed: 200 average time/residue: 0.0909 time to fit residues: 24.8537 Evaluate side-chains 185 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 421 MET Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 58 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 30 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 48 optimal weight: 0.3980 chunk 112 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 172 ASN E 249 HIS E 439 ASN ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.131256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.102157 restraints weight = 10519.344| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.95 r_work: 0.2832 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9003 Z= 0.196 Angle : 0.605 10.063 12204 Z= 0.306 Chirality : 0.043 0.141 1388 Planarity : 0.004 0.044 1537 Dihedral : 5.713 80.803 1228 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 4.72 % Allowed : 20.55 % Favored : 74.74 % 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: -2.83 (0.23), residues: 1144 helix: -0.09 (0.32), residues: 268 sheet: -1.58 (0.26), residues: 368 loop : -3.13 (0.23), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 175 TYR 0.013 0.001 TYR E 61 PHE 0.020 0.001 PHE C 431 TRP 0.014 0.001 TRP C 20 HIS 0.008 0.001 HIS C 226 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 8999) covalent geometry : angle 0.60425 (12196) SS BOND : bond 0.00377 ( 4) SS BOND : angle 1.03703 ( 8) hydrogen bonds : bond 0.03476 ( 311) hydrogen bonds : angle 5.08654 ( 918) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 161 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 151 MET cc_start: 0.6742 (mmt) cc_final: 0.6237 (mmp) REVERT: C 172 ASN cc_start: 0.8617 (OUTLIER) cc_final: 0.8406 (t0) REVERT: C 175 ARG cc_start: 0.6606 (ptt-90) cc_final: 0.6169 (ptt-90) REVERT: C 332 TYR cc_start: 0.8618 (t80) cc_final: 0.8332 (t80) REVERT: C 349 MET cc_start: 0.5303 (ttm) cc_final: 0.4735 (tmm) REVERT: C 416 ARG cc_start: 0.7722 (ttm-80) cc_final: 0.7157 (mtm110) REVERT: C 449 PHE cc_start: 0.6389 (t80) cc_final: 0.5185 (m-10) REVERT: C 456 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8153 (mp) REVERT: C 477 LEU cc_start: 0.8700 (mt) cc_final: 0.8371 (mt) REVERT: D 4 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8506 (mm) REVERT: D 23 ARG cc_start: 0.8997 (ttm170) cc_final: 0.8687 (mtm-85) REVERT: E 66 SER cc_start: 0.9136 (m) cc_final: 0.8685 (t) REVERT: E 175 ARG cc_start: 0.8147 (ptp90) cc_final: 0.7710 (ptp90) REVERT: E 454 LYS cc_start: 0.8496 (ttpp) cc_final: 0.8248 (tttm) REVERT: F 10 ARG cc_start: 0.9134 (mmt90) cc_final: 0.8697 (mmm160) outliers start: 45 outliers final: 38 residues processed: 192 average time/residue: 0.0832 time to fit residues: 22.4789 Evaluate side-chains 191 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 421 MET Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 58 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 172 ASN E 439 ASN ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.129944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.100897 restraints weight = 10458.802| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.96 r_work: 0.2820 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9003 Z= 0.216 Angle : 0.622 9.447 12204 Z= 0.313 Chirality : 0.044 0.139 1388 Planarity : 0.004 0.044 1537 Dihedral : 5.807 83.400 1228 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 6.08 % Allowed : 22.01 % Favored : 71.91 % 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: -2.62 (0.24), residues: 1144 helix: -0.06 (0.32), residues: 268 sheet: -1.42 (0.27), residues: 366 loop : -2.93 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 175 TYR 0.018 0.002 TYR E 332 PHE 0.020 0.001 PHE C 431 TRP 0.012 0.001 TRP E 400 HIS 0.009 0.001 HIS C 226 Details of bonding type rmsd covalent geometry : bond 0.00522 ( 8999) covalent geometry : angle 0.62164 (12196) SS BOND : bond 0.00544 ( 4) SS BOND : angle 0.92970 ( 8) hydrogen bonds : bond 0.03508 ( 311) hydrogen bonds : angle 5.04492 ( 918) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 151 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 71 ASP cc_start: 0.8940 (t0) cc_final: 0.8622 (t0) REVERT: C 73 ARG cc_start: 0.8494 (mmt180) cc_final: 0.7762 (mmm-85) REVERT: C 151 MET cc_start: 0.6493 (mmt) cc_final: 0.6069 (mmp) REVERT: C 175 ARG cc_start: 0.6743 (ptt-90) cc_final: 0.5759 (ptt-90) REVERT: C 277 MET cc_start: 0.8581 (ttm) cc_final: 0.8347 (ttm) REVERT: C 349 MET cc_start: 0.5095 (ttm) cc_final: 0.4539 (tmm) REVERT: C 416 ARG cc_start: 0.7735 (ttm-80) cc_final: 0.7179 (ttp80) REVERT: C 449 PHE cc_start: 0.6379 (t80) cc_final: 0.5231 (m-10) REVERT: C 456 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8149 (mp) REVERT: C 477 LEU cc_start: 0.8668 (mt) cc_final: 0.8402 (mt) REVERT: D 4 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8547 (mm) REVERT: D 23 ARG cc_start: 0.9007 (ttm170) cc_final: 0.8677 (mtm-85) REVERT: E 55 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8216 (mp0) REVERT: E 66 SER cc_start: 0.9223 (m) cc_final: 0.8782 (t) REVERT: E 454 LYS cc_start: 0.8502 (ttpp) cc_final: 0.8256 (tttm) REVERT: F 10 ARG cc_start: 0.9158 (mmt90) cc_final: 0.8743 (mmm160) outliers start: 58 outliers final: 45 residues processed: 191 average time/residue: 0.0836 time to fit residues: 22.3251 Evaluate side-chains 195 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 147 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 421 MET Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 58 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 45 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 78 optimal weight: 0.7980 chunk 108 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.131939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.102774 restraints weight = 10346.407| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.98 r_work: 0.2865 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9003 Z= 0.135 Angle : 0.563 8.467 12204 Z= 0.283 Chirality : 0.041 0.140 1388 Planarity : 0.004 0.043 1537 Dihedral : 5.533 79.911 1228 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 4.93 % Allowed : 23.90 % Favored : 71.17 % 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: -2.37 (0.24), residues: 1144 helix: 0.09 (0.32), residues: 270 sheet: -1.22 (0.27), residues: 368 loop : -2.80 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 73 TYR 0.012 0.001 TYR E 305 PHE 0.012 0.001 PHE C 431 TRP 0.009 0.001 TRP E 400 HIS 0.007 0.001 HIS C 226 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8999) covalent geometry : angle 0.56292 (12196) SS BOND : bond 0.00307 ( 4) SS BOND : angle 0.70731 ( 8) hydrogen bonds : bond 0.03061 ( 311) hydrogen bonds : angle 4.77073 ( 918) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 147 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 71 ASP cc_start: 0.8867 (t0) cc_final: 0.8587 (t0) REVERT: C 151 MET cc_start: 0.6437 (mmt) cc_final: 0.5975 (mmp) REVERT: C 175 ARG cc_start: 0.6687 (ptt-90) cc_final: 0.5407 (mtm-85) REVERT: C 349 MET cc_start: 0.5031 (ttm) cc_final: 0.4653 (tmm) REVERT: C 416 ARG cc_start: 0.7718 (ttm-80) cc_final: 0.7170 (ttp80) REVERT: C 455 SER cc_start: 0.8983 (t) cc_final: 0.8748 (t) REVERT: C 456 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8142 (mp) REVERT: D 4 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8507 (mm) REVERT: D 23 ARG cc_start: 0.8956 (ttm170) cc_final: 0.8665 (mtm-85) REVERT: E 55 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8169 (mp0) REVERT: E 66 SER cc_start: 0.9201 (m) cc_final: 0.8746 (t) REVERT: E 151 MET cc_start: 0.4777 (mmt) cc_final: 0.4532 (mpp) REVERT: E 454 LYS cc_start: 0.8531 (ttpp) cc_final: 0.8302 (tttm) REVERT: F 10 ARG cc_start: 0.9109 (mmt90) cc_final: 0.8744 (mmm160) outliers start: 47 outliers final: 39 residues processed: 180 average time/residue: 0.0916 time to fit residues: 22.7213 Evaluate side-chains 185 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 58 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.130085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.101327 restraints weight = 10419.089| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.93 r_work: 0.2845 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9003 Z= 0.169 Angle : 0.585 8.326 12204 Z= 0.294 Chirality : 0.042 0.136 1388 Planarity : 0.004 0.042 1537 Dihedral : 5.587 81.281 1228 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 5.66 % Allowed : 23.17 % Favored : 71.17 % 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: -2.25 (0.24), residues: 1144 helix: 0.14 (0.32), residues: 270 sheet: -1.12 (0.27), residues: 366 loop : -2.71 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 164 TYR 0.015 0.001 TYR E 305 PHE 0.017 0.001 PHE C 431 TRP 0.011 0.001 TRP E 400 HIS 0.008 0.001 HIS C 226 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 8999) covalent geometry : angle 0.58502 (12196) SS BOND : bond 0.00381 ( 4) SS BOND : angle 0.89005 ( 8) hydrogen bonds : bond 0.03185 ( 311) hydrogen bonds : angle 4.75804 ( 918) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 147 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 15 MET cc_start: 0.7160 (OUTLIER) cc_final: 0.6704 (mtp) REVERT: C 71 ASP cc_start: 0.8917 (t0) cc_final: 0.8649 (t0) REVERT: C 151 MET cc_start: 0.6683 (mmt) cc_final: 0.6271 (mmp) REVERT: C 175 ARG cc_start: 0.6815 (ptt-90) cc_final: 0.5542 (ptt-90) REVERT: C 349 MET cc_start: 0.5065 (ttm) cc_final: 0.4713 (tmm) REVERT: C 416 ARG cc_start: 0.7684 (ttm-80) cc_final: 0.7113 (ttp80) REVERT: C 449 PHE cc_start: 0.6631 (t80) cc_final: 0.5350 (m-10) REVERT: C 455 SER cc_start: 0.9047 (t) cc_final: 0.8840 (t) REVERT: C 456 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8202 (mp) REVERT: D 4 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8545 (mm) REVERT: D 23 ARG cc_start: 0.8979 (ttm170) cc_final: 0.8698 (mtm-85) REVERT: E 55 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8196 (mp0) REVERT: E 66 SER cc_start: 0.9200 (m) cc_final: 0.8727 (t) REVERT: E 454 LYS cc_start: 0.8620 (ttpp) cc_final: 0.8388 (tttm) REVERT: F 10 ARG cc_start: 0.9117 (mmt90) cc_final: 0.8746 (mmm160) outliers start: 54 outliers final: 44 residues processed: 183 average time/residue: 0.0884 time to fit residues: 22.4958 Evaluate side-chains 194 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 146 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 421 MET Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 494 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 58 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.0980 chunk 51 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 48 optimal weight: 0.1980 chunk 7 optimal weight: 0.9980 chunk 87 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 GLN ** F 7 HIS ** 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 = 0.3407 r_free = 0.3407 target = 0.133677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.104482 restraints weight = 10278.143| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.95 r_work: 0.2928 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9003 Z= 0.092 Angle : 0.530 8.357 12204 Z= 0.265 Chirality : 0.040 0.133 1388 Planarity : 0.003 0.041 1537 Dihedral : 5.177 74.557 1227 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 4.40 % Allowed : 24.42 % Favored : 71.17 % 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: -1.98 (0.25), residues: 1144 helix: 0.30 (0.33), residues: 272 sheet: -0.83 (0.28), residues: 338 loop : -2.55 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 73 TYR 0.016 0.001 TYR E 305 PHE 0.009 0.001 PHE C 453 TRP 0.011 0.001 TRP D 19 HIS 0.006 0.001 HIS C 226 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 8999) covalent geometry : angle 0.53035 (12196) SS BOND : bond 0.00233 ( 4) SS BOND : angle 0.56501 ( 8) hydrogen bonds : bond 0.02730 ( 311) hydrogen bonds : angle 4.37612 ( 918) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 159 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: C 15 MET cc_start: 0.6497 (OUTLIER) cc_final: 0.6261 (mtt) REVERT: C 71 ASP cc_start: 0.8662 (t0) cc_final: 0.8390 (t0) REVERT: C 151 MET cc_start: 0.6869 (mmt) cc_final: 0.6513 (mmp) REVERT: C 175 ARG cc_start: 0.6657 (ptt-90) cc_final: 0.5417 (mtm-85) REVERT: C 349 MET cc_start: 0.4622 (ttm) cc_final: 0.4352 (tmm) REVERT: C 416 ARG cc_start: 0.7682 (ttm-80) cc_final: 0.7127 (mtm110) REVERT: C 456 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7815 (mp) REVERT: D 4 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8709 (mm) REVERT: D 23 ARG cc_start: 0.8924 (ttm170) cc_final: 0.8624 (mtm-85) REVERT: E 66 SER cc_start: 0.9181 (m) cc_final: 0.8753 (t) REVERT: E 164 ARG cc_start: 0.8271 (mtp85) cc_final: 0.8022 (mmm160) REVERT: E 345 MET cc_start: 0.8964 (mtp) cc_final: 0.8668 (mtm) REVERT: E 454 LYS cc_start: 0.8626 (ttpp) cc_final: 0.8394 (tttm) REVERT: F 10 ARG cc_start: 0.9045 (mmt90) cc_final: 0.8733 (mmm160) outliers start: 42 outliers final: 32 residues processed: 189 average time/residue: 0.0870 time to fit residues: 22.9016 Evaluate side-chains 178 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 15 MET Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 421 MET Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 58 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 69 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.127391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.098967 restraints weight = 10425.569| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.90 r_work: 0.2828 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9003 Z= 0.227 Angle : 0.635 9.330 12204 Z= 0.318 Chirality : 0.044 0.146 1388 Planarity : 0.004 0.044 1537 Dihedral : 5.626 84.254 1227 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 4.82 % Allowed : 24.53 % Favored : 70.65 % 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: -2.03 (0.25), residues: 1144 helix: 0.12 (0.32), residues: 274 sheet: -0.97 (0.27), residues: 366 loop : -2.47 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 164 TYR 0.022 0.002 TYR E 305 PHE 0.020 0.002 PHE C 431 TRP 0.012 0.001 TRP E 400 HIS 0.009 0.001 HIS C 226 Details of bonding type rmsd covalent geometry : bond 0.00549 ( 8999) covalent geometry : angle 0.63484 (12196) SS BOND : bond 0.00464 ( 4) SS BOND : angle 0.97968 ( 8) hydrogen bonds : bond 0.03426 ( 311) hydrogen bonds : angle 4.70367 ( 918) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 149 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 ASP cc_start: 0.8932 (t0) cc_final: 0.8690 (t0) REVERT: C 151 MET cc_start: 0.6920 (mmt) cc_final: 0.6535 (mmm) REVERT: C 175 ARG cc_start: 0.6866 (ptt-90) cc_final: 0.5562 (mtm-85) REVERT: C 349 MET cc_start: 0.4948 (ttm) cc_final: 0.4442 (tmm) REVERT: C 416 ARG cc_start: 0.7616 (ttm-80) cc_final: 0.7018 (ttp80) REVERT: C 449 PHE cc_start: 0.6267 (t80) cc_final: 0.5216 (m-10) REVERT: C 456 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8243 (mp) REVERT: D 4 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8705 (mm) REVERT: D 23 ARG cc_start: 0.8989 (ttm170) cc_final: 0.8738 (mtm-85) REVERT: E 66 SER cc_start: 0.9181 (m) cc_final: 0.8747 (t) REVERT: E 151 MET cc_start: 0.5539 (OUTLIER) cc_final: 0.3881 (mpp) REVERT: E 454 LYS cc_start: 0.8625 (ttpp) cc_final: 0.8394 (tttm) REVERT: F 10 ARG cc_start: 0.9112 (mmt90) cc_final: 0.8755 (mmm160) outliers start: 46 outliers final: 39 residues processed: 180 average time/residue: 0.0836 time to fit residues: 21.1915 Evaluate side-chains 186 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 144 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 421 MET Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 494 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 58 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 56 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 chunk 8 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 GLN ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.130251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.102895 restraints weight = 10365.752| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.85 r_work: 0.2900 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9003 Z= 0.132 Angle : 0.564 9.391 12204 Z= 0.283 Chirality : 0.041 0.135 1388 Planarity : 0.004 0.042 1537 Dihedral : 5.413 80.816 1227 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 4.40 % Allowed : 25.16 % Favored : 70.44 % 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: -1.82 (0.25), residues: 1144 helix: 0.38 (0.33), residues: 264 sheet: -0.82 (0.28), residues: 354 loop : -2.34 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 73 TYR 0.015 0.001 TYR E 305 PHE 0.013 0.001 PHE C 431 TRP 0.010 0.001 TRP E 400 HIS 0.007 0.001 HIS C 226 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8999) covalent geometry : angle 0.56394 (12196) SS BOND : bond 0.00310 ( 4) SS BOND : angle 0.72813 ( 8) hydrogen bonds : bond 0.03006 ( 311) hydrogen bonds : angle 4.50750 ( 918) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 71 ASP cc_start: 0.8731 (t0) cc_final: 0.8519 (t0) REVERT: C 151 MET cc_start: 0.6822 (mmt) cc_final: 0.6359 (mmm) REVERT: C 175 ARG cc_start: 0.6761 (ptt-90) cc_final: 0.5507 (mtm-85) REVERT: C 349 MET cc_start: 0.4640 (ttm) cc_final: 0.4313 (tmm) REVERT: C 416 ARG cc_start: 0.7584 (ttm-80) cc_final: 0.7046 (ttp80) REVERT: C 456 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8073 (mp) REVERT: C 478 ASN cc_start: 0.7738 (m-40) cc_final: 0.6812 (p0) REVERT: D 4 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8639 (mm) REVERT: D 23 ARG cc_start: 0.8927 (ttm170) cc_final: 0.8592 (mtm-85) REVERT: E 66 SER cc_start: 0.9160 (m) cc_final: 0.8726 (t) REVERT: E 101 TRP cc_start: 0.8991 (m-10) cc_final: 0.8770 (m-10) REVERT: E 151 MET cc_start: 0.5666 (OUTLIER) cc_final: 0.4341 (mpp) REVERT: E 454 LYS cc_start: 0.8608 (ttpp) cc_final: 0.8381 (tttm) REVERT: F 10 ARG cc_start: 0.9084 (mmt90) cc_final: 0.8722 (mmm160) outliers start: 42 outliers final: 36 residues processed: 171 average time/residue: 0.0859 time to fit residues: 20.5359 Evaluate side-chains 179 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 140 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 421 MET Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 494 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 58 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 14 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.127930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.098547 restraints weight = 10361.876| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.95 r_work: 0.2838 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9003 Z= 0.194 Angle : 0.612 9.515 12204 Z= 0.306 Chirality : 0.043 0.140 1388 Planarity : 0.004 0.044 1537 Dihedral : 5.553 83.649 1227 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 4.82 % Allowed : 25.05 % Favored : 70.13 % 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: -1.86 (0.25), residues: 1144 helix: 0.20 (0.32), residues: 274 sheet: -0.79 (0.28), residues: 354 loop : -2.36 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 164 TYR 0.018 0.002 TYR E 305 PHE 0.019 0.001 PHE C 431 TRP 0.011 0.001 TRP E 400 HIS 0.009 0.001 HIS C 226 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 8999) covalent geometry : angle 0.61185 (12196) SS BOND : bond 0.00430 ( 4) SS BOND : angle 0.91349 ( 8) hydrogen bonds : bond 0.03251 ( 311) hydrogen bonds : angle 4.61985 ( 918) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2185.40 seconds wall clock time: 38 minutes 14.90 seconds (2294.90 seconds total)