Starting phenix.real_space_refine on Fri Feb 6 04:26:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gxj_51664/02_2026/9gxj_51664.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gxj_51664/02_2026/9gxj_51664.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gxj_51664/02_2026/9gxj_51664.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gxj_51664/02_2026/9gxj_51664.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gxj_51664/02_2026/9gxj_51664.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gxj_51664/02_2026/9gxj_51664.map" } resolution = 2.3 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= 0.014 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 56 5.16 5 C 14126 2.51 5 N 3864 2.21 5 O 4319 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22365 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3195 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 23, 'TRANS': 382} Chain breaks: 2 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 3.46, per 1000 atoms: 0.15 Number of scatterers: 22365 At special positions: 0 Unit cell: (175.028, 173.054, 112.518, 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 56 16.00 O 4319 8.00 N 3864 7.00 C 14126 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 159 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS D 159 " - pdb=" SG CYS D 164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 164 " distance=2.03 Simple disulfide: pdb=" SG CYS F 159 " - pdb=" SG CYS F 164 " distance=2.03 Simple disulfide: pdb=" SG CYS G 159 " - pdb=" SG CYS G 164 " 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: 1.75 Conformation dependent library (CDL) restraints added in 1.1 seconds 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5166 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 16 sheets defined 23.2% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 removed outlier: 3.770A pdb=" N LEU A 9 " --> pdb=" O PRO A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 34 removed outlier: 3.534A pdb=" N VAL A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 41 Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 97 through 107 Processing helix chain 'A' and resid 108 through 124 removed outlier: 5.422A pdb=" N LYS A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Proline residue: A 115 - end of helix Processing helix chain 'A' and resid 350 through 353 Processing helix chain 'A' and resid 354 through 361 Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.511A pdb=" N VAL A 368 " --> pdb=" O PRO A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 381 removed outlier: 3.547A pdb=" N THR A 376 " --> pdb=" O ASP A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 393 Processing helix chain 'B' and resid 5 through 9 removed outlier: 3.770A pdb=" N LEU B 9 " --> pdb=" O PRO B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 34 removed outlier: 3.534A pdb=" N VAL B 34 " --> pdb=" O GLU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 41 Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 97 through 107 Processing helix chain 'B' and resid 108 through 124 removed outlier: 5.422A pdb=" N LYS B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Proline residue: B 115 - end of helix Processing helix chain 'B' and resid 350 through 353 Processing helix chain 'B' and resid 354 through 361 Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.511A pdb=" N VAL B 368 " --> pdb=" O PRO B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 381 removed outlier: 3.547A pdb=" N THR B 376 " --> pdb=" O ASP B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 393 Processing helix chain 'C' and resid 5 through 9 removed outlier: 3.770A pdb=" N LEU C 9 " --> pdb=" O PRO C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 34 removed outlier: 3.534A pdb=" N VAL C 34 " --> pdb=" O GLU C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 41 Processing helix chain 'C' and resid 58 through 62 Processing helix chain 'C' and resid 97 through 107 Processing helix chain 'C' and resid 108 through 124 removed outlier: 5.422A pdb=" N LYS C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) Proline residue: C 115 - end of helix Processing helix chain 'C' and resid 350 through 353 Processing helix chain 'C' and resid 354 through 361 Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.511A pdb=" N VAL C 368 " --> pdb=" O PRO C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 381 removed outlier: 3.547A pdb=" N THR C 376 " --> pdb=" O ASP C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 393 Processing helix chain 'D' and resid 5 through 9 removed outlier: 3.770A pdb=" N LEU D 9 " --> pdb=" O PRO D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 34 removed outlier: 3.534A pdb=" N VAL D 34 " --> pdb=" O GLU D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 41 Processing helix chain 'D' and resid 58 through 62 Processing helix chain 'D' and resid 97 through 107 Processing helix chain 'D' and resid 108 through 124 removed outlier: 5.422A pdb=" N LYS D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Proline residue: D 115 - end of helix Processing helix chain 'D' and resid 350 through 353 Processing helix chain 'D' and resid 354 through 361 Processing helix chain 'D' and resid 364 through 368 removed outlier: 3.512A pdb=" N VAL D 368 " --> pdb=" O PRO D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 381 removed outlier: 3.547A pdb=" N THR D 376 " --> pdb=" O ASP D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 393 Processing helix chain 'E' and resid 5 through 9 removed outlier: 3.770A pdb=" N LEU E 9 " --> pdb=" O PRO E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 34 removed outlier: 3.533A pdb=" N VAL E 34 " --> pdb=" O GLU E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 41 Processing helix chain 'E' and resid 58 through 62 Processing helix chain 'E' and resid 97 through 107 Processing helix chain 'E' and resid 108 through 124 removed outlier: 5.422A pdb=" N LYS E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Proline residue: E 115 - end of helix Processing helix chain 'E' and resid 350 through 353 Processing helix chain 'E' and resid 354 through 361 Processing helix chain 'E' and resid 364 through 368 removed outlier: 3.511A pdb=" N VAL E 368 " --> pdb=" O PRO E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 381 removed outlier: 3.546A pdb=" N THR E 376 " --> pdb=" O ASP E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 393 Processing helix chain 'F' and resid 5 through 9 removed outlier: 3.770A pdb=" N LEU F 9 " --> pdb=" O PRO F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 34 removed outlier: 3.534A pdb=" N VAL F 34 " --> pdb=" O GLU F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 41 Processing helix chain 'F' and resid 58 through 62 Processing helix chain 'F' and resid 97 through 107 Processing helix chain 'F' and resid 108 through 124 removed outlier: 5.422A pdb=" N LYS F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) Proline residue: F 115 - end of helix Processing helix chain 'F' and resid 350 through 353 Processing helix chain 'F' and resid 354 through 361 Processing helix chain 'F' and resid 364 through 368 removed outlier: 3.512A pdb=" N VAL F 368 " --> pdb=" O PRO F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 381 removed outlier: 3.547A pdb=" N THR F 376 " --> pdb=" O ASP F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 393 Processing helix chain 'G' and resid 5 through 9 removed outlier: 3.770A pdb=" N LEU G 9 " --> pdb=" O PRO G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 34 removed outlier: 3.534A pdb=" N VAL G 34 " --> pdb=" O GLU G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 41 Processing helix chain 'G' and resid 58 through 62 Processing helix chain 'G' and resid 97 through 107 Processing helix chain 'G' and resid 108 through 124 removed outlier: 5.422A pdb=" N LYS G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) Proline residue: G 115 - end of helix Processing helix chain 'G' and resid 350 through 353 Processing helix chain 'G' and resid 354 through 361 Processing helix chain 'G' and resid 364 through 368 removed outlier: 3.511A pdb=" N VAL G 368 " --> pdb=" O PRO G 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 372 through 381 removed outlier: 3.547A pdb=" N THR G 376 " --> pdb=" O ASP G 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 381 through 393 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.565A pdb=" N PHE A 12 " --> pdb=" O THR A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 49 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 96 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 91 through 96 current: chain 'A' and resid 149 through 153 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 169 through 179 current: chain 'A' and resid 289 through 321 removed outlier: 3.585A pdb=" N TYR A 314 " --> pdb=" O ILE A 345 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 338 through 345 current: chain 'B' and resid 149 through 153 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 169 through 179 current: chain 'B' and resid 289 through 321 removed outlier: 3.585A pdb=" N TYR B 314 " --> pdb=" O ILE B 345 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 338 through 345 current: chain 'C' and resid 149 through 153 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 169 through 179 current: chain 'C' and resid 289 through 321 removed outlier: 3.586A pdb=" N TYR C 314 " --> pdb=" O ILE C 345 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 338 through 345 current: chain 'D' and resid 149 through 153 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 169 through 179 current: chain 'D' and resid 289 through 321 removed outlier: 3.585A pdb=" N TYR D 314 " --> pdb=" O ILE D 345 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 338 through 345 current: chain 'E' and resid 149 through 153 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 169 through 179 current: chain 'E' and resid 289 through 321 removed outlier: 3.585A pdb=" N TYR E 314 " --> pdb=" O ILE E 345 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 338 through 345 current: chain 'F' and resid 149 through 153 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 169 through 179 current: chain 'F' and resid 289 through 321 removed outlier: 3.585A pdb=" N TYR F 314 " --> pdb=" O ILE F 345 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 338 through 345 current: chain 'G' and resid 149 through 153 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 169 through 179 current: chain 'G' and resid 289 through 321 removed outlier: 3.585A pdb=" N TYR G 314 " --> pdb=" O ILE G 345 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 215 through 243 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.564A pdb=" N PHE B 12 " --> pdb=" O THR B 73 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 48 through 49 Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.564A pdb=" N PHE C 12 " --> pdb=" O THR C 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 48 through 49 Processing sheet with id=AA9, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.565A pdb=" N PHE D 12 " --> pdb=" O THR D 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 48 through 49 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.564A pdb=" N PHE E 12 " --> pdb=" O THR E 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 48 through 49 Processing sheet with id=AB4, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.565A pdb=" N PHE F 12 " --> pdb=" O THR F 73 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 48 through 49 Processing sheet with id=AB6, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.564A pdb=" N PHE G 12 " --> pdb=" O THR G 73 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 48 through 49 840 hydrogen bonds defined for protein. 2331 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: 3.90 Time building geometry restraints manager: 2.42 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: 7104 1.34 - 1.46: 5468 1.46 - 1.58: 10332 1.58 - 1.70: 0 1.70 - 1.81: 91 Bond restraints: 22995 Sorted by residual: bond pdb=" C TYR F 76 " pdb=" N PRO F 77 " ideal model delta sigma weight residual 1.331 1.377 -0.045 1.27e-02 6.20e+03 1.28e+01 bond pdb=" CA GLY C 399 " pdb=" C GLY C 399 " ideal model delta sigma weight residual 1.517 1.537 -0.020 7.00e-03 2.04e+04 7.80e+00 bond pdb=" CA GLY E 399 " pdb=" C GLY E 399 " ideal model delta sigma weight residual 1.517 1.537 -0.019 7.00e-03 2.04e+04 7.51e+00 bond pdb=" CA GLY G 399 " pdb=" C GLY G 399 " ideal model delta sigma weight residual 1.517 1.536 -0.019 7.00e-03 2.04e+04 7.40e+00 bond pdb=" N PRO A 80 " pdb=" CA PRO A 80 " ideal model delta sigma weight residual 1.465 1.498 -0.032 1.19e-02 7.06e+03 7.39e+00 ... (remaining 22990 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 29635 1.23 - 2.45: 1468 2.45 - 3.68: 220 3.68 - 4.90: 45 4.90 - 6.13: 20 Bond angle restraints: 31388 Sorted by residual: angle pdb=" C PRO F 77 " pdb=" CA PRO F 77 " pdb=" CB PRO F 77 " ideal model delta sigma weight residual 111.56 107.91 3.65 1.27e+00 6.20e-01 8.28e+00 angle pdb=" N PRO F 77 " pdb=" CA PRO F 77 " pdb=" C PRO F 77 " ideal model delta sigma weight residual 111.15 115.47 -4.32 1.58e+00 4.01e-01 7.48e+00 angle pdb=" C PRO E 77 " pdb=" CA PRO E 77 " pdb=" CB PRO E 77 " ideal model delta sigma weight residual 111.56 108.15 3.41 1.27e+00 6.20e-01 7.20e+00 angle pdb=" C PRO C 77 " pdb=" CA PRO C 77 " pdb=" CB PRO C 77 " ideal model delta sigma weight residual 111.56 108.17 3.39 1.27e+00 6.20e-01 7.14e+00 angle pdb=" C PRO A 77 " pdb=" CA PRO A 77 " pdb=" CB PRO A 77 " ideal model delta sigma weight residual 111.56 108.17 3.39 1.27e+00 6.20e-01 7.13e+00 ... (remaining 31383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.51: 12201 13.51 - 27.02: 812 27.02 - 40.53: 203 40.53 - 54.03: 84 54.03 - 67.54: 35 Dihedral angle restraints: 13335 sinusoidal: 5208 harmonic: 8127 Sorted by residual: dihedral pdb=" CA ASP A 350 " pdb=" CB ASP A 350 " pdb=" CG ASP A 350 " pdb=" OD1 ASP A 350 " ideal model delta sinusoidal sigma weight residual -30.00 -85.14 55.14 1 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" CA ASP C 350 " pdb=" CB ASP C 350 " pdb=" CG ASP C 350 " pdb=" OD1 ASP C 350 " ideal model delta sinusoidal sigma weight residual -30.00 -85.12 55.12 1 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" CA ASP B 350 " pdb=" CB ASP B 350 " pdb=" CG ASP B 350 " pdb=" OD1 ASP B 350 " ideal model delta sinusoidal sigma weight residual -30.00 -85.09 55.09 1 2.00e+01 2.50e-03 1.03e+01 ... (remaining 13332 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2121 0.035 - 0.071: 747 0.071 - 0.106: 243 0.106 - 0.141: 165 0.141 - 0.176: 21 Chirality restraints: 3297 Sorted by residual: chirality pdb=" CA TYR G 76 " pdb=" N TYR G 76 " pdb=" C TYR G 76 " pdb=" CB TYR G 76 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.77e-01 chirality pdb=" CA TYR B 76 " pdb=" N TYR B 76 " pdb=" C TYR B 76 " pdb=" CB TYR B 76 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.62e-01 chirality pdb=" CA TYR A 76 " pdb=" N TYR A 76 " pdb=" C TYR A 76 " pdb=" CB TYR A 76 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.53e-01 ... (remaining 3294 not shown) Planarity restraints: 4088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 291 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO C 292 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 292 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 292 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 291 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO E 292 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO E 292 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 292 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 291 " 0.022 5.00e-02 4.00e+02 3.33e-02 1.78e+00 pdb=" N PRO G 292 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO G 292 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO G 292 " 0.018 5.00e-02 4.00e+02 ... (remaining 4085 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4233 2.78 - 3.31: 18785 3.31 - 3.84: 35579 3.84 - 4.37: 41880 4.37 - 4.90: 74763 Nonbonded interactions: 175240 Sorted by model distance: nonbonded pdb=" OD1 ASP B 209 " pdb=" NH2 ARG B 288 " model vdw 2.251 3.120 nonbonded pdb=" OD1 ASP F 209 " pdb=" NH2 ARG F 288 " model vdw 2.251 3.120 nonbonded pdb=" OD1 ASP G 209 " pdb=" NH2 ARG G 288 " model vdw 2.251 3.120 nonbonded pdb=" OD1 ASP E 209 " pdb=" NH2 ARG E 288 " model vdw 2.252 3.120 nonbonded pdb=" OD1 ASP A 209 " pdb=" NH2 ARG A 288 " model vdw 2.252 3.120 ... (remaining 175235 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 7.560 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: 0.030 Extract box with map and model: 0.630 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 19.060 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 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 : 0.004 0.045 23002 Z= 0.274 Angle : 0.607 6.127 31402 Z= 0.358 Chirality : 0.047 0.176 3297 Planarity : 0.004 0.033 4088 Dihedral : 11.148 67.542 8148 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.63 % Allowed : 5.56 % Favored : 91.81 % 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: 0.09 (0.15), residues: 2800 helix: 0.66 (0.23), residues: 497 sheet: 0.97 (0.15), residues: 1036 loop : -0.96 (0.15), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 194 TYR 0.015 0.002 TYR F 61 PHE 0.012 0.002 PHE E 321 TRP 0.008 0.001 TRP C 370 HIS 0.003 0.001 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00438 (22995) covalent geometry : angle 0.60670 (31388) SS BOND : bond 0.00158 ( 7) SS BOND : angle 0.58034 ( 14) hydrogen bonds : bond 0.26015 ( 840) hydrogen bonds : angle 8.34178 ( 2331) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 384 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7798 (mt-10) REVERT: A 116 THR cc_start: 0.8701 (m) cc_final: 0.8353 (p) REVERT: A 185 LYS cc_start: 0.8399 (mttt) cc_final: 0.8049 (mttp) REVERT: A 195 GLN cc_start: 0.8650 (mt0) cc_final: 0.8124 (mm110) REVERT: A 233 TYR cc_start: 0.7441 (m-80) cc_final: 0.6671 (t80) REVERT: A 378 GLN cc_start: 0.8539 (tt0) cc_final: 0.8326 (tt0) REVERT: B 57 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.6017 (ptp) REVERT: B 116 THR cc_start: 0.8699 (m) cc_final: 0.8330 (p) REVERT: B 185 LYS cc_start: 0.8453 (mttt) cc_final: 0.8132 (mttm) REVERT: B 195 GLN cc_start: 0.8651 (mt0) cc_final: 0.8178 (mm-40) REVERT: B 233 TYR cc_start: 0.7503 (m-80) cc_final: 0.6733 (t80) REVERT: B 378 GLN cc_start: 0.8587 (tt0) cc_final: 0.8353 (tt0) REVERT: C 116 THR cc_start: 0.8694 (m) cc_final: 0.8318 (p) REVERT: C 185 LYS cc_start: 0.8415 (mttt) cc_final: 0.8001 (mttm) REVERT: C 195 GLN cc_start: 0.8617 (mt0) cc_final: 0.8079 (mm110) REVERT: C 233 TYR cc_start: 0.7512 (m-80) cc_final: 0.6709 (t80) REVERT: D 116 THR cc_start: 0.8742 (m) cc_final: 0.8356 (p) REVERT: D 185 LYS cc_start: 0.8479 (mttt) cc_final: 0.8113 (mttp) REVERT: D 195 GLN cc_start: 0.8661 (mt0) cc_final: 0.8126 (mm110) REVERT: D 233 TYR cc_start: 0.7484 (m-80) cc_final: 0.6620 (t80) REVERT: E 2 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8098 (mt-10) REVERT: E 116 THR cc_start: 0.8676 (m) cc_final: 0.8282 (p) REVERT: E 185 LYS cc_start: 0.8514 (mttt) cc_final: 0.8217 (mttp) REVERT: E 195 GLN cc_start: 0.8597 (mt0) cc_final: 0.8074 (mm110) REVERT: E 233 TYR cc_start: 0.7434 (m-80) cc_final: 0.6669 (t80) REVERT: E 378 GLN cc_start: 0.8566 (tt0) cc_final: 0.8365 (tt0) REVERT: F 30 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7923 (mt-10) REVERT: F 185 LYS cc_start: 0.8422 (mttt) cc_final: 0.8096 (mttm) REVERT: F 195 GLN cc_start: 0.8617 (mt0) cc_final: 0.8090 (mm110) REVERT: F 233 TYR cc_start: 0.7485 (m-80) cc_final: 0.6646 (t80) REVERT: F 378 GLN cc_start: 0.8508 (tt0) cc_final: 0.8296 (tt0) REVERT: G 30 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7917 (mt-10) REVERT: G 57 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.6091 (ptp) REVERT: G 116 THR cc_start: 0.8740 (m) cc_final: 0.8370 (p) REVERT: G 185 LYS cc_start: 0.8462 (mttt) cc_final: 0.8117 (mttp) REVERT: G 195 GLN cc_start: 0.8600 (mt0) cc_final: 0.8109 (mm-40) REVERT: G 233 TYR cc_start: 0.7510 (m-80) cc_final: 0.6709 (t80) outliers start: 63 outliers final: 19 residues processed: 426 average time/residue: 0.6867 time to fit residues: 329.7639 Evaluate side-chains 335 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 314 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 263 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 263 GLN Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 171 LYS Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 262 ASN Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain G residue 57 MET Chi-restraints excluded: chain G residue 262 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.0570 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN A 263 GLN B 44 GLN B 231 ASN B 263 GLN C 231 ASN C 263 GLN D 231 ASN D 243 ASN D 263 GLN E 231 ASN E 263 GLN F 8 GLN F 44 GLN F 231 ASN F 263 GLN G 231 ASN G 263 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.097368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.068072 restraints weight = 31761.244| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.30 r_work: 0.2665 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2559 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23002 Z= 0.147 Angle : 0.571 6.882 31402 Z= 0.313 Chirality : 0.046 0.139 3297 Planarity : 0.004 0.032 4088 Dihedral : 5.614 71.361 3141 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.43 % Allowed : 9.77 % Favored : 86.80 % 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: 0.58 (0.15), residues: 2800 helix: 0.90 (0.22), residues: 497 sheet: 1.24 (0.15), residues: 1008 loop : -0.50 (0.16), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 10 TYR 0.011 0.001 TYR E 61 PHE 0.014 0.002 PHE A 321 TRP 0.009 0.001 TRP F 359 HIS 0.003 0.001 HIS C 186 Details of bonding type rmsd covalent geometry : bond 0.00292 (22995) covalent geometry : angle 0.57110 (31388) SS BOND : bond 0.00113 ( 7) SS BOND : angle 0.50279 ( 14) hydrogen bonds : bond 0.05638 ( 840) hydrogen bonds : angle 5.00756 ( 2331) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 310 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.6162 (ttp-170) cc_final: 0.5893 (ttp-170) REVERT: A 27 ASN cc_start: 0.7487 (p0) cc_final: 0.7267 (p0) REVERT: A 57 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.6082 (ptp) REVERT: A 116 THR cc_start: 0.8767 (m) cc_final: 0.8436 (p) REVERT: A 185 LYS cc_start: 0.8556 (mttt) cc_final: 0.8199 (mttp) REVERT: A 195 GLN cc_start: 0.8760 (mt0) cc_final: 0.8276 (mm110) REVERT: A 233 TYR cc_start: 0.7472 (m-80) cc_final: 0.6924 (t80) REVERT: A 242 LYS cc_start: 0.7040 (ttmt) cc_final: 0.6784 (tppp) REVERT: A 262 ASN cc_start: 0.7958 (OUTLIER) cc_final: 0.7647 (p0) REVERT: B 10 ARG cc_start: 0.3974 (ptt-90) cc_final: 0.3772 (ptt-90) REVERT: B 116 THR cc_start: 0.8782 (m) cc_final: 0.8478 (p) REVERT: B 185 LYS cc_start: 0.8648 (mttt) cc_final: 0.8277 (mttp) REVERT: B 195 GLN cc_start: 0.8710 (mt0) cc_final: 0.8298 (mm-40) REVERT: B 233 TYR cc_start: 0.7401 (m-80) cc_final: 0.6930 (t80) REVERT: B 237 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6942 (pm20) REVERT: B 262 ASN cc_start: 0.8116 (OUTLIER) cc_final: 0.7734 (p0) REVERT: B 378 GLN cc_start: 0.8631 (tt0) cc_final: 0.8411 (tt0) REVERT: C 29 GLU cc_start: 0.7659 (mp0) cc_final: 0.7255 (tp30) REVERT: C 116 THR cc_start: 0.8780 (m) cc_final: 0.8449 (p) REVERT: C 185 LYS cc_start: 0.8574 (mttt) cc_final: 0.8151 (mttm) REVERT: C 195 GLN cc_start: 0.8738 (mt0) cc_final: 0.8250 (mm110) REVERT: C 233 TYR cc_start: 0.7387 (m-80) cc_final: 0.6814 (t80) REVERT: C 237 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7455 (mp0) REVERT: C 262 ASN cc_start: 0.8064 (OUTLIER) cc_final: 0.7667 (p0) REVERT: D 29 GLU cc_start: 0.7717 (mp0) cc_final: 0.7291 (tp30) REVERT: D 116 THR cc_start: 0.8770 (m) cc_final: 0.8455 (p) REVERT: D 171 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8215 (mmtp) REVERT: D 185 LYS cc_start: 0.8626 (mttt) cc_final: 0.8237 (mttp) REVERT: D 195 GLN cc_start: 0.8759 (mt0) cc_final: 0.8267 (mm110) REVERT: D 233 TYR cc_start: 0.7361 (m-80) cc_final: 0.6807 (t80) REVERT: D 242 LYS cc_start: 0.6936 (OUTLIER) cc_final: 0.6734 (tppp) REVERT: D 262 ASN cc_start: 0.8084 (OUTLIER) cc_final: 0.7764 (p0) REVERT: D 307 GLU cc_start: 0.9000 (pt0) cc_final: 0.8788 (pt0) REVERT: E 29 GLU cc_start: 0.7667 (mp0) cc_final: 0.7286 (tp30) REVERT: E 116 THR cc_start: 0.8774 (m) cc_final: 0.8396 (p) REVERT: E 185 LYS cc_start: 0.8702 (mttt) cc_final: 0.8381 (mttp) REVERT: E 195 GLN cc_start: 0.8670 (mt0) cc_final: 0.8204 (mm110) REVERT: E 233 TYR cc_start: 0.7346 (m-80) cc_final: 0.6884 (t80) REVERT: E 242 LYS cc_start: 0.6982 (ttmt) cc_final: 0.6731 (tppp) REVERT: E 262 ASN cc_start: 0.8123 (OUTLIER) cc_final: 0.7762 (p0) REVERT: F 116 THR cc_start: 0.8784 (m) cc_final: 0.8471 (p) REVERT: F 185 LYS cc_start: 0.8585 (mttt) cc_final: 0.8262 (mttm) REVERT: F 195 GLN cc_start: 0.8670 (mt0) cc_final: 0.8194 (mm110) REVERT: F 233 TYR cc_start: 0.7360 (m-80) cc_final: 0.6782 (t80) REVERT: F 262 ASN cc_start: 0.8068 (OUTLIER) cc_final: 0.7753 (p0) REVERT: G 10 ARG cc_start: 0.4030 (ptt-90) cc_final: 0.3830 (ptt-90) REVERT: G 57 MET cc_start: 0.7507 (OUTLIER) cc_final: 0.6236 (ptp) REVERT: G 116 THR cc_start: 0.8765 (m) cc_final: 0.8427 (p) REVERT: G 185 LYS cc_start: 0.8632 (mttt) cc_final: 0.8268 (mttp) REVERT: G 195 GLN cc_start: 0.8677 (mt0) cc_final: 0.8241 (mm-40) REVERT: G 233 TYR cc_start: 0.7455 (m-80) cc_final: 0.6929 (t80) REVERT: G 262 ASN cc_start: 0.8012 (OUTLIER) cc_final: 0.7696 (p0) outliers start: 82 outliers final: 26 residues processed: 350 average time/residue: 0.7573 time to fit residues: 295.5947 Evaluate side-chains 277 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 238 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 263 GLN Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 171 LYS Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 242 LYS Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 263 GLN Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 262 ASN Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 57 MET Chi-restraints excluded: chain G residue 237 GLU Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 262 ASN Chi-restraints excluded: chain G residue 408 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 144 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 232 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 200 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 201 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 52 ASN E 52 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.092602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.063218 restraints weight = 32038.003| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 2.29 r_work: 0.2573 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2466 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 23002 Z= 0.309 Angle : 0.716 7.327 31402 Z= 0.399 Chirality : 0.053 0.157 3297 Planarity : 0.006 0.043 4088 Dihedral : 5.830 67.540 3120 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.38 % Allowed : 10.48 % Favored : 86.13 % 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: 0.66 (0.15), residues: 2800 helix: 1.00 (0.23), residues: 490 sheet: 1.36 (0.15), residues: 1064 loop : -0.62 (0.16), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 394 TYR 0.015 0.002 TYR C 61 PHE 0.024 0.003 PHE G 321 TRP 0.015 0.002 TRP B 54 HIS 0.006 0.002 HIS C 186 Details of bonding type rmsd covalent geometry : bond 0.00723 (22995) covalent geometry : angle 0.71623 (31388) SS BOND : bond 0.00147 ( 7) SS BOND : angle 0.64214 ( 14) hydrogen bonds : bond 0.08021 ( 840) hydrogen bonds : angle 4.92554 ( 2331) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 228 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.6090 (ttp-170) cc_final: 0.5777 (mpp-170) REVERT: A 29 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7422 (tp30) REVERT: A 57 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.6406 (ptp) REVERT: A 185 LYS cc_start: 0.8609 (mttt) cc_final: 0.8246 (mttp) REVERT: A 195 GLN cc_start: 0.8847 (mt0) cc_final: 0.8380 (mm-40) REVERT: A 233 TYR cc_start: 0.7562 (m-80) cc_final: 0.7026 (t80) REVERT: A 262 ASN cc_start: 0.8268 (OUTLIER) cc_final: 0.7877 (p0) REVERT: B 24 ARG cc_start: 0.6067 (ttp-170) cc_final: 0.5723 (mpp-170) REVERT: B 116 THR cc_start: 0.8845 (m) cc_final: 0.8479 (p) REVERT: B 185 LYS cc_start: 0.8625 (mttt) cc_final: 0.8335 (mttm) REVERT: B 195 GLN cc_start: 0.8811 (mt0) cc_final: 0.8361 (mm-40) REVERT: B 233 TYR cc_start: 0.7586 (m-80) cc_final: 0.7049 (t80) REVERT: B 237 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: B 378 GLN cc_start: 0.8635 (tt0) cc_final: 0.8383 (tt0) REVERT: C 24 ARG cc_start: 0.5896 (ttp-170) cc_final: 0.5605 (mpp-170) REVERT: C 116 THR cc_start: 0.8862 (m) cc_final: 0.8492 (p) REVERT: C 185 LYS cc_start: 0.8636 (mttt) cc_final: 0.8196 (mttp) REVERT: C 195 GLN cc_start: 0.8786 (mt0) cc_final: 0.8253 (mm-40) REVERT: C 233 TYR cc_start: 0.7605 (m-80) cc_final: 0.6945 (t80) REVERT: D 24 ARG cc_start: 0.5953 (ttp-170) cc_final: 0.5647 (mpp-170) REVERT: D 116 THR cc_start: 0.8899 (m) cc_final: 0.8544 (p) REVERT: D 171 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8334 (mmtp) REVERT: D 185 LYS cc_start: 0.8692 (mttt) cc_final: 0.8351 (mttp) REVERT: D 195 GLN cc_start: 0.8813 (mt0) cc_final: 0.8345 (mm-40) REVERT: D 233 TYR cc_start: 0.7600 (m-80) cc_final: 0.6846 (t80) REVERT: D 262 ASN cc_start: 0.8426 (OUTLIER) cc_final: 0.8088 (p0) REVERT: E 10 ARG cc_start: 0.3838 (ptt-90) cc_final: 0.3626 (ptt-90) REVERT: E 116 THR cc_start: 0.8870 (m) cc_final: 0.8491 (p) REVERT: E 185 LYS cc_start: 0.8682 (mttt) cc_final: 0.8371 (mttp) REVERT: E 195 GLN cc_start: 0.8764 (mt0) cc_final: 0.8329 (mm-40) REVERT: E 233 TYR cc_start: 0.7571 (m-80) cc_final: 0.6933 (t80) REVERT: E 242 LYS cc_start: 0.7112 (ttmt) cc_final: 0.6793 (tppp) REVERT: E 262 ASN cc_start: 0.8370 (OUTLIER) cc_final: 0.8100 (p0) REVERT: F 2 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8352 (mt-10) REVERT: F 57 MET cc_start: 0.7702 (ptp) cc_final: 0.6153 (ptp) REVERT: F 171 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8176 (mmtp) REVERT: F 185 LYS cc_start: 0.8645 (mttt) cc_final: 0.8312 (mttm) REVERT: F 195 GLN cc_start: 0.8776 (mt0) cc_final: 0.8205 (mm110) REVERT: F 233 TYR cc_start: 0.7567 (m-80) cc_final: 0.6885 (t80) REVERT: F 262 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.7971 (p0) REVERT: G 57 MET cc_start: 0.7639 (ptp) cc_final: 0.6502 (ptp) REVERT: G 116 THR cc_start: 0.8830 (m) cc_final: 0.8482 (p) REVERT: G 185 LYS cc_start: 0.8694 (mttt) cc_final: 0.8331 (mttp) REVERT: G 195 GLN cc_start: 0.8791 (mt0) cc_final: 0.8357 (mm-40) REVERT: G 233 TYR cc_start: 0.7634 (m-80) cc_final: 0.7075 (t80) REVERT: G 262 ASN cc_start: 0.8331 (OUTLIER) cc_final: 0.7986 (p0) outliers start: 81 outliers final: 35 residues processed: 279 average time/residue: 0.7276 time to fit residues: 228.3042 Evaluate side-chains 266 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 221 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLN Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 171 LYS Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 256 SER Chi-restraints excluded: chain F residue 262 ASN Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 171 LYS Chi-restraints excluded: chain G residue 237 GLU Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 262 ASN Chi-restraints excluded: chain G residue 408 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 3 optimal weight: 5.9990 chunk 193 optimal weight: 0.9980 chunk 204 optimal weight: 0.3980 chunk 263 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 256 optimal weight: 0.8980 chunk 140 optimal weight: 0.7980 chunk 171 optimal weight: 3.9990 chunk 15 optimal weight: 0.0770 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 ASN E 52 ASN E 79 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.097370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.068237 restraints weight = 31674.758| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 2.30 r_work: 0.2671 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 23002 Z= 0.126 Angle : 0.521 7.019 31402 Z= 0.285 Chirality : 0.044 0.140 3297 Planarity : 0.004 0.030 4088 Dihedral : 4.436 31.055 3103 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.51 % Allowed : 11.36 % Favored : 86.13 % 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: 0.72 (0.15), residues: 2800 helix: 0.98 (0.22), residues: 497 sheet: 1.29 (0.15), residues: 1071 loop : -0.43 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 10 TYR 0.008 0.001 TYR A 348 PHE 0.009 0.001 PHE G 321 TRP 0.008 0.001 TRP F 103 HIS 0.002 0.001 HIS F 186 Details of bonding type rmsd covalent geometry : bond 0.00217 (22995) covalent geometry : angle 0.52103 (31388) SS BOND : bond 0.00043 ( 7) SS BOND : angle 0.19038 ( 14) hydrogen bonds : bond 0.04450 ( 840) hydrogen bonds : angle 4.66005 ( 2331) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 235 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.6056 (ttp-170) cc_final: 0.5661 (mpp-170) REVERT: A 57 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.6433 (ptp) REVERT: A 116 THR cc_start: 0.8778 (m) cc_final: 0.8471 (p) REVERT: A 185 LYS cc_start: 0.8539 (mttt) cc_final: 0.8176 (mttp) REVERT: A 195 GLN cc_start: 0.8764 (mt0) cc_final: 0.8264 (mm110) REVERT: A 233 TYR cc_start: 0.7348 (m-80) cc_final: 0.6980 (t80) REVERT: A 263 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8142 (mm-40) REVERT: B 24 ARG cc_start: 0.6031 (ttp-170) cc_final: 0.5659 (mpp-170) REVERT: B 57 MET cc_start: 0.7653 (ptp) cc_final: 0.6377 (ptp) REVERT: B 116 THR cc_start: 0.8765 (m) cc_final: 0.8468 (p) REVERT: B 185 LYS cc_start: 0.8583 (mttt) cc_final: 0.8259 (mttp) REVERT: B 195 GLN cc_start: 0.8725 (mt0) cc_final: 0.8288 (mm-40) REVERT: B 233 TYR cc_start: 0.7339 (m-80) cc_final: 0.6952 (t80) REVERT: B 263 GLN cc_start: 0.8086 (mp10) cc_final: 0.7750 (tt0) REVERT: B 378 GLN cc_start: 0.8585 (tt0) cc_final: 0.8346 (tt0) REVERT: C 24 ARG cc_start: 0.5835 (ttp-170) cc_final: 0.5555 (mpp-170) REVERT: C 116 THR cc_start: 0.8771 (m) cc_final: 0.8458 (p) REVERT: C 185 LYS cc_start: 0.8573 (mttt) cc_final: 0.8189 (mttp) REVERT: C 195 GLN cc_start: 0.8734 (mt0) cc_final: 0.8228 (mm110) REVERT: C 233 TYR cc_start: 0.7293 (m-80) cc_final: 0.6896 (t80) REVERT: C 262 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7893 (p0) REVERT: D 116 THR cc_start: 0.8775 (m) cc_final: 0.8496 (p) REVERT: D 185 LYS cc_start: 0.8633 (mttt) cc_final: 0.8305 (mttp) REVERT: D 195 GLN cc_start: 0.8740 (mt0) cc_final: 0.8218 (mm110) REVERT: D 233 TYR cc_start: 0.7325 (m-80) cc_final: 0.6798 (t80) REVERT: D 262 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.7933 (p0) REVERT: E 10 ARG cc_start: 0.3856 (ptt-90) cc_final: 0.3565 (ptt-90) REVERT: E 116 THR cc_start: 0.8761 (m) cc_final: 0.8387 (p) REVERT: E 185 LYS cc_start: 0.8622 (mttt) cc_final: 0.8319 (mttp) REVERT: E 195 GLN cc_start: 0.8681 (mt0) cc_final: 0.8183 (mm110) REVERT: E 233 TYR cc_start: 0.7273 (m-80) cc_final: 0.6807 (t80) REVERT: E 242 LYS cc_start: 0.7066 (ttmt) cc_final: 0.6774 (tppp) REVERT: F 2 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8220 (mt-10) REVERT: F 57 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.6142 (ptp) REVERT: F 116 THR cc_start: 0.8745 (m) cc_final: 0.8468 (p) REVERT: F 185 LYS cc_start: 0.8582 (mttt) cc_final: 0.8255 (mttm) REVERT: F 195 GLN cc_start: 0.8697 (mt0) cc_final: 0.8178 (mm110) REVERT: F 233 TYR cc_start: 0.7321 (m-80) cc_final: 0.6740 (t80) REVERT: F 262 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7843 (p0) REVERT: G 57 MET cc_start: 0.7605 (ptp) cc_final: 0.6469 (ptp) REVERT: G 116 THR cc_start: 0.8759 (m) cc_final: 0.8433 (p) REVERT: G 185 LYS cc_start: 0.8644 (mttt) cc_final: 0.8282 (mttp) REVERT: G 195 GLN cc_start: 0.8703 (mt0) cc_final: 0.8298 (mm-40) REVERT: G 233 TYR cc_start: 0.7355 (m-80) cc_final: 0.6946 (t80) REVERT: G 262 ASN cc_start: 0.8096 (OUTLIER) cc_final: 0.7813 (p0) outliers start: 60 outliers final: 26 residues processed: 258 average time/residue: 0.7677 time to fit residues: 222.7049 Evaluate side-chains 256 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 223 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain E residue 8 GLN Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 262 ASN Chi-restraints excluded: chain G residue 42 MET Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 171 LYS Chi-restraints excluded: chain G residue 262 ASN Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain G residue 408 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 40 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 58 optimal weight: 0.4980 chunk 201 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 271 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 227 optimal weight: 0.5980 chunk 243 optimal weight: 7.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN B 231 ASN C 52 ASN C 231 ASN F 231 ASN G 231 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.094975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.065775 restraints weight = 31475.249| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 2.28 r_work: 0.2622 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 23002 Z= 0.182 Angle : 0.578 6.977 31402 Z= 0.319 Chirality : 0.047 0.142 3297 Planarity : 0.005 0.033 4088 Dihedral : 4.485 29.685 3095 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.51 % Allowed : 11.86 % Favored : 85.63 % 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: 0.76 (0.15), residues: 2800 helix: 1.10 (0.23), residues: 497 sheet: 1.34 (0.15), residues: 1071 loop : -0.47 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 10 TYR 0.010 0.001 TYR E 61 PHE 0.016 0.002 PHE F 321 TRP 0.010 0.001 TRP G 359 HIS 0.004 0.001 HIS C 186 Details of bonding type rmsd covalent geometry : bond 0.00382 (22995) covalent geometry : angle 0.57821 (31388) SS BOND : bond 0.00101 ( 7) SS BOND : angle 0.32480 ( 14) hydrogen bonds : bond 0.05773 ( 840) hydrogen bonds : angle 4.58577 ( 2331) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 222 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.6019 (ttp-170) cc_final: 0.5633 (mpp-170) REVERT: A 57 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.6551 (ptp) REVERT: A 116 THR cc_start: 0.8818 (m) cc_final: 0.8464 (p) REVERT: A 185 LYS cc_start: 0.8567 (mttt) cc_final: 0.8204 (mttp) REVERT: A 195 GLN cc_start: 0.8819 (mt0) cc_final: 0.8383 (mm-40) REVERT: A 233 TYR cc_start: 0.7460 (m-80) cc_final: 0.7026 (t80) REVERT: A 262 ASN cc_start: 0.8054 (OUTLIER) cc_final: 0.7714 (p0) REVERT: A 263 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8233 (mm110) REVERT: B 24 ARG cc_start: 0.6076 (ttp-170) cc_final: 0.5562 (mpp-170) REVERT: B 57 MET cc_start: 0.7742 (ptp) cc_final: 0.6501 (ptp) REVERT: B 116 THR cc_start: 0.8822 (m) cc_final: 0.8483 (p) REVERT: B 185 LYS cc_start: 0.8600 (mttt) cc_final: 0.8316 (mttm) REVERT: B 195 GLN cc_start: 0.8798 (mt0) cc_final: 0.8369 (mm-40) REVERT: B 233 TYR cc_start: 0.7452 (m-80) cc_final: 0.6976 (t80) REVERT: B 262 ASN cc_start: 0.8236 (OUTLIER) cc_final: 0.7870 (p0) REVERT: B 378 GLN cc_start: 0.8610 (tt0) cc_final: 0.8373 (tt0) REVERT: C 24 ARG cc_start: 0.5888 (ttp-170) cc_final: 0.5601 (mpp-170) REVERT: C 116 THR cc_start: 0.8818 (m) cc_final: 0.8465 (p) REVERT: C 185 LYS cc_start: 0.8590 (mttt) cc_final: 0.8158 (mttp) REVERT: C 195 GLN cc_start: 0.8767 (mt0) cc_final: 0.8252 (mm110) REVERT: C 233 TYR cc_start: 0.7437 (m-80) cc_final: 0.6829 (t80) REVERT: C 242 LYS cc_start: 0.7184 (tppt) cc_final: 0.6978 (tppp) REVERT: C 262 ASN cc_start: 0.8296 (OUTLIER) cc_final: 0.7944 (p0) REVERT: D 24 ARG cc_start: 0.4638 (mpp-170) cc_final: 0.4278 (mpp-170) REVERT: D 57 MET cc_start: 0.7571 (ptp) cc_final: 0.6248 (ptp) REVERT: D 116 THR cc_start: 0.8836 (m) cc_final: 0.8507 (p) REVERT: D 171 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8285 (mmtp) REVERT: D 185 LYS cc_start: 0.8647 (mttt) cc_final: 0.8319 (mttp) REVERT: D 195 GLN cc_start: 0.8788 (mt0) cc_final: 0.8251 (mm110) REVERT: D 233 TYR cc_start: 0.7446 (m-80) cc_final: 0.6835 (t80) REVERT: D 262 ASN cc_start: 0.8289 (OUTLIER) cc_final: 0.7989 (p0) REVERT: E 116 THR cc_start: 0.8804 (m) cc_final: 0.8407 (p) REVERT: E 185 LYS cc_start: 0.8645 (mttt) cc_final: 0.8339 (mttp) REVERT: E 195 GLN cc_start: 0.8727 (mt0) cc_final: 0.8214 (mm110) REVERT: E 233 TYR cc_start: 0.7397 (m-80) cc_final: 0.6865 (t80) REVERT: E 262 ASN cc_start: 0.8257 (OUTLIER) cc_final: 0.7899 (p0) REVERT: F 2 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8266 (mt-10) REVERT: F 57 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.6303 (ptp) REVERT: F 171 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8075 (mmtp) REVERT: F 185 LYS cc_start: 0.8622 (mttt) cc_final: 0.8299 (mttm) REVERT: F 195 GLN cc_start: 0.8750 (mt0) cc_final: 0.8217 (mm110) REVERT: F 233 TYR cc_start: 0.7411 (m-80) cc_final: 0.6825 (t80) REVERT: F 262 ASN cc_start: 0.8200 (OUTLIER) cc_final: 0.7919 (p0) REVERT: G 57 MET cc_start: 0.7669 (ptp) cc_final: 0.6488 (ptp) REVERT: G 116 THR cc_start: 0.8791 (m) cc_final: 0.8434 (p) REVERT: G 185 LYS cc_start: 0.8658 (mttt) cc_final: 0.8291 (mttp) REVERT: G 195 GLN cc_start: 0.8748 (mt0) cc_final: 0.8327 (mm-40) REVERT: G 233 TYR cc_start: 0.7486 (m-80) cc_final: 0.7008 (t80) REVERT: G 262 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7899 (p0) outliers start: 60 outliers final: 32 residues processed: 252 average time/residue: 0.7295 time to fit residues: 207.7943 Evaluate side-chains 262 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 218 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLN Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 171 LYS Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain E residue 8 GLN Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 262 ASN Chi-restraints excluded: chain G residue 8 GLN Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 171 LYS Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 262 ASN Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain G residue 408 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 128 optimal weight: 6.9990 chunk 270 optimal weight: 0.7980 chunk 163 optimal weight: 7.9990 chunk 158 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 252 optimal weight: 9.9990 chunk 268 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 204 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.093716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.064479 restraints weight = 32044.117| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 2.29 r_work: 0.2597 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2491 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 23002 Z= 0.220 Angle : 0.624 6.690 31402 Z= 0.346 Chirality : 0.049 0.144 3297 Planarity : 0.005 0.035 4088 Dihedral : 4.666 27.782 3095 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.80 % Allowed : 11.53 % Favored : 85.67 % 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: 0.68 (0.15), residues: 2800 helix: 0.99 (0.23), residues: 497 sheet: 1.33 (0.15), residues: 1071 loop : -0.57 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 10 TYR 0.010 0.002 TYR E 61 PHE 0.019 0.002 PHE G 321 TRP 0.011 0.002 TRP F 359 HIS 0.004 0.001 HIS C 186 Details of bonding type rmsd covalent geometry : bond 0.00482 (22995) covalent geometry : angle 0.62364 (31388) SS BOND : bond 0.00133 ( 7) SS BOND : angle 0.43575 ( 14) hydrogen bonds : bond 0.06427 ( 840) hydrogen bonds : angle 4.66045 ( 2331) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 218 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.6027 (ttp-170) cc_final: 0.5629 (mpp-170) REVERT: A 57 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.6639 (ptp) REVERT: A 116 THR cc_start: 0.8842 (m) cc_final: 0.8480 (p) REVERT: A 185 LYS cc_start: 0.8565 (mttt) cc_final: 0.8195 (mttp) REVERT: A 195 GLN cc_start: 0.8842 (mt0) cc_final: 0.8360 (mm-40) REVERT: A 233 TYR cc_start: 0.7537 (m-80) cc_final: 0.7081 (t80) REVERT: A 262 ASN cc_start: 0.8148 (OUTLIER) cc_final: 0.7794 (p0) REVERT: A 263 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8272 (mm110) REVERT: B 24 ARG cc_start: 0.6070 (ttp-170) cc_final: 0.5481 (mpp-170) REVERT: B 57 MET cc_start: 0.7800 (ptp) cc_final: 0.6484 (ptp) REVERT: B 116 THR cc_start: 0.8830 (m) cc_final: 0.8501 (p) REVERT: B 185 LYS cc_start: 0.8602 (mttt) cc_final: 0.8268 (mttp) REVERT: B 195 GLN cc_start: 0.8801 (mt0) cc_final: 0.8363 (mm-40) REVERT: B 233 TYR cc_start: 0.7547 (m-80) cc_final: 0.7075 (t80) REVERT: B 262 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.7916 (p0) REVERT: B 378 GLN cc_start: 0.8621 (tt0) cc_final: 0.8393 (tt0) REVERT: C 78 THR cc_start: 0.7392 (OUTLIER) cc_final: 0.7137 (m) REVERT: C 116 THR cc_start: 0.8857 (m) cc_final: 0.8512 (p) REVERT: C 185 LYS cc_start: 0.8609 (mttt) cc_final: 0.8198 (mttp) REVERT: C 195 GLN cc_start: 0.8795 (mt0) cc_final: 0.8270 (mm110) REVERT: C 233 TYR cc_start: 0.7541 (m-80) cc_final: 0.6956 (t80) REVERT: D 57 MET cc_start: 0.7643 (ptp) cc_final: 0.6298 (ptp) REVERT: D 116 THR cc_start: 0.8857 (m) cc_final: 0.8527 (p) REVERT: D 171 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8287 (mmtp) REVERT: D 185 LYS cc_start: 0.8656 (mttt) cc_final: 0.8321 (mttp) REVERT: D 195 GLN cc_start: 0.8807 (mt0) cc_final: 0.8321 (mm-40) REVERT: D 233 TYR cc_start: 0.7522 (m-80) cc_final: 0.6859 (t80) REVERT: E 116 THR cc_start: 0.8831 (m) cc_final: 0.8437 (p) REVERT: E 185 LYS cc_start: 0.8646 (mttt) cc_final: 0.8336 (mttp) REVERT: E 195 GLN cc_start: 0.8744 (mt0) cc_final: 0.8298 (mm-40) REVERT: E 233 TYR cc_start: 0.7487 (m-80) cc_final: 0.6934 (t80) REVERT: E 242 LYS cc_start: 0.7151 (tppp) cc_final: 0.6931 (tppp) REVERT: E 262 ASN cc_start: 0.8320 (OUTLIER) cc_final: 0.8065 (p0) REVERT: F 2 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8309 (mt-10) REVERT: F 57 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.6394 (ptp) REVERT: F 78 THR cc_start: 0.8375 (OUTLIER) cc_final: 0.8171 (t) REVERT: F 171 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8138 (mmtp) REVERT: F 185 LYS cc_start: 0.8620 (mttt) cc_final: 0.8291 (mttm) REVERT: F 195 GLN cc_start: 0.8746 (mt0) cc_final: 0.8269 (mm-40) REVERT: F 233 TYR cc_start: 0.7513 (m-80) cc_final: 0.6905 (t80) REVERT: F 238 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8102 (ttpp) REVERT: F 262 ASN cc_start: 0.8269 (OUTLIER) cc_final: 0.7983 (p0) REVERT: F 378 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8191 (tt0) REVERT: G 57 MET cc_start: 0.7766 (ptp) cc_final: 0.6579 (ptp) REVERT: G 116 THR cc_start: 0.8819 (m) cc_final: 0.8467 (p) REVERT: G 185 LYS cc_start: 0.8656 (mttt) cc_final: 0.8219 (mttp) REVERT: G 195 GLN cc_start: 0.8771 (mt0) cc_final: 0.8321 (mm-40) REVERT: G 233 TYR cc_start: 0.7542 (m-80) cc_final: 0.7073 (t80) outliers start: 67 outliers final: 31 residues processed: 257 average time/residue: 0.7428 time to fit residues: 215.8559 Evaluate side-chains 259 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 215 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 171 LYS Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 171 LYS Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain E residue 8 GLN Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain F residue 262 ASN Chi-restraints excluded: chain F residue 378 GLN Chi-restraints excluded: chain G residue 8 GLN Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 171 LYS Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain G residue 408 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 72 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 273 optimal weight: 0.8980 chunk 262 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN F 52 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.092649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.063480 restraints weight = 31868.773| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 2.27 r_work: 0.2578 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 23002 Z= 0.265 Angle : 0.672 6.795 31402 Z= 0.374 Chirality : 0.051 0.150 3297 Planarity : 0.005 0.038 4088 Dihedral : 4.783 26.131 3089 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.92 % Allowed : 11.53 % Favored : 85.55 % 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: 0.65 (0.15), residues: 2800 helix: 1.04 (0.23), residues: 490 sheet: 1.42 (0.15), residues: 1064 loop : -0.71 (0.16), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 24 TYR 0.012 0.002 TYR B 357 PHE 0.022 0.002 PHE G 321 TRP 0.012 0.002 TRP G 54 HIS 0.005 0.001 HIS C 186 Details of bonding type rmsd covalent geometry : bond 0.00604 (22995) covalent geometry : angle 0.67173 (31388) SS BOND : bond 0.00176 ( 7) SS BOND : angle 0.52579 ( 14) hydrogen bonds : bond 0.07096 ( 840) hydrogen bonds : angle 4.73565 ( 2331) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 217 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.6030 (ttp-170) cc_final: 0.5590 (mpp-170) REVERT: A 57 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.6692 (ptp) REVERT: A 116 THR cc_start: 0.8890 (m) cc_final: 0.8514 (p) REVERT: A 185 LYS cc_start: 0.8583 (mttt) cc_final: 0.8197 (mttp) REVERT: A 195 GLN cc_start: 0.8858 (mt0) cc_final: 0.8442 (mm-40) REVERT: A 233 TYR cc_start: 0.7566 (m-80) cc_final: 0.7096 (t80) REVERT: A 262 ASN cc_start: 0.8269 (OUTLIER) cc_final: 0.7904 (p0) REVERT: A 263 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8289 (mm110) REVERT: B 57 MET cc_start: 0.7845 (ptp) cc_final: 0.6613 (ptp) REVERT: B 116 THR cc_start: 0.8865 (m) cc_final: 0.8528 (p) REVERT: B 185 LYS cc_start: 0.8610 (mttt) cc_final: 0.8319 (mttm) REVERT: B 195 GLN cc_start: 0.8835 (mt0) cc_final: 0.8389 (mm-40) REVERT: B 233 TYR cc_start: 0.7593 (m-80) cc_final: 0.7111 (t80) REVERT: B 378 GLN cc_start: 0.8643 (tt0) cc_final: 0.8411 (tt0) REVERT: C 116 THR cc_start: 0.8878 (m) cc_final: 0.8522 (p) REVERT: C 185 LYS cc_start: 0.8632 (mttt) cc_final: 0.8236 (mttp) REVERT: C 195 GLN cc_start: 0.8833 (mt0) cc_final: 0.8322 (mm-40) REVERT: C 233 TYR cc_start: 0.7581 (m-80) cc_final: 0.6940 (t80) REVERT: C 237 GLU cc_start: 0.7719 (mp0) cc_final: 0.7311 (mp0) REVERT: C 262 ASN cc_start: 0.8358 (OUTLIER) cc_final: 0.7932 (p0) REVERT: C 263 GLN cc_start: 0.8324 (mp10) cc_final: 0.7848 (mt0) REVERT: D 57 MET cc_start: 0.7637 (ptp) cc_final: 0.6262 (ptp) REVERT: D 116 THR cc_start: 0.8906 (m) cc_final: 0.8564 (p) REVERT: D 171 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8335 (mmtp) REVERT: D 185 LYS cc_start: 0.8669 (mttt) cc_final: 0.8239 (mttp) REVERT: D 195 GLN cc_start: 0.8828 (mt0) cc_final: 0.8354 (mm-40) REVERT: D 233 TYR cc_start: 0.7569 (m-80) cc_final: 0.6865 (t80) REVERT: D 262 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.8080 (p0) REVERT: E 10 ARG cc_start: 0.3485 (ptt-90) cc_final: 0.3261 (ptt-90) REVERT: E 116 THR cc_start: 0.8871 (m) cc_final: 0.8502 (p) REVERT: E 185 LYS cc_start: 0.8665 (mttt) cc_final: 0.8349 (mttp) REVERT: E 195 GLN cc_start: 0.8791 (mt0) cc_final: 0.8343 (mm-40) REVERT: E 233 TYR cc_start: 0.7538 (m-80) cc_final: 0.6926 (t80) REVERT: E 242 LYS cc_start: 0.7183 (OUTLIER) cc_final: 0.6958 (tppp) REVERT: F 2 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8324 (mt-10) REVERT: F 57 MET cc_start: 0.7865 (ptp) cc_final: 0.6410 (ptp) REVERT: F 171 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8156 (mmtp) REVERT: F 185 LYS cc_start: 0.8636 (mttt) cc_final: 0.8305 (mttm) REVERT: F 195 GLN cc_start: 0.8789 (mt0) cc_final: 0.8274 (mm-40) REVERT: F 233 TYR cc_start: 0.7572 (m-80) cc_final: 0.6917 (t80) REVERT: F 238 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8151 (ttpp) REVERT: F 378 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8209 (tt0) REVERT: G 57 MET cc_start: 0.7796 (ptp) cc_final: 0.6583 (ptp) REVERT: G 116 THR cc_start: 0.8845 (m) cc_final: 0.8492 (p) REVERT: G 185 LYS cc_start: 0.8670 (mttt) cc_final: 0.8250 (mttp) REVERT: G 195 GLN cc_start: 0.8819 (mt0) cc_final: 0.8389 (mm-40) REVERT: G 233 TYR cc_start: 0.7605 (m-80) cc_final: 0.7098 (t80) outliers start: 70 outliers final: 31 residues processed: 257 average time/residue: 0.7224 time to fit residues: 210.3003 Evaluate side-chains 248 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 207 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 171 LYS Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain E residue 8 GLN Chi-restraints excluded: chain E residue 42 MET Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain F residue 378 GLN Chi-restraints excluded: chain G residue 8 GLN Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 171 LYS Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain G residue 408 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 62 optimal weight: 9.9990 chunk 166 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 84 optimal weight: 0.7980 chunk 216 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 267 optimal weight: 0.4980 chunk 163 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 ASN D 52 ASN E 243 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.096518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.067679 restraints weight = 31747.836| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 2.20 r_work: 0.2643 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 23002 Z= 0.146 Angle : 0.543 6.444 31402 Z= 0.298 Chirality : 0.046 0.144 3297 Planarity : 0.004 0.030 4088 Dihedral : 4.293 16.727 3087 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.13 % Allowed : 12.45 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.73 (0.15), residues: 2800 helix: 1.03 (0.23), residues: 497 sheet: 1.38 (0.15), residues: 1071 loop : -0.56 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 10 TYR 0.008 0.001 TYR A 348 PHE 0.010 0.001 PHE G 321 TRP 0.009 0.001 TRP A 265 HIS 0.002 0.001 HIS D 186 Details of bonding type rmsd covalent geometry : bond 0.00288 (22995) covalent geometry : angle 0.54280 (31388) SS BOND : bond 0.00063 ( 7) SS BOND : angle 0.30456 ( 14) hydrogen bonds : bond 0.04676 ( 840) hydrogen bonds : angle 4.57992 ( 2331) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 213 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.5937 (ttp-170) cc_final: 0.5593 (mpp-170) REVERT: A 57 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.6623 (ptp) REVERT: A 116 THR cc_start: 0.8731 (m) cc_final: 0.8393 (p) REVERT: A 185 LYS cc_start: 0.8499 (mttt) cc_final: 0.8122 (mttp) REVERT: A 195 GLN cc_start: 0.8774 (mt0) cc_final: 0.8278 (mm110) REVERT: A 233 TYR cc_start: 0.7314 (m-80) cc_final: 0.6975 (t80) REVERT: A 262 ASN cc_start: 0.7974 (OUTLIER) cc_final: 0.7625 (p0) REVERT: B 57 MET cc_start: 0.7807 (ptp) cc_final: 0.6428 (ptp) REVERT: B 116 THR cc_start: 0.8732 (m) cc_final: 0.8421 (p) REVERT: B 185 LYS cc_start: 0.8535 (mttt) cc_final: 0.8195 (mttp) REVERT: B 195 GLN cc_start: 0.8759 (mt0) cc_final: 0.8311 (mm-40) REVERT: B 233 TYR cc_start: 0.7268 (m-80) cc_final: 0.6913 (t80) REVERT: B 262 ASN cc_start: 0.8157 (OUTLIER) cc_final: 0.7774 (p0) REVERT: B 378 GLN cc_start: 0.8516 (tt0) cc_final: 0.8279 (tt0) REVERT: C 116 THR cc_start: 0.8734 (m) cc_final: 0.8418 (p) REVERT: C 185 LYS cc_start: 0.8541 (mttt) cc_final: 0.8137 (mttp) REVERT: C 195 GLN cc_start: 0.8757 (mt0) cc_final: 0.8216 (mm110) REVERT: C 233 TYR cc_start: 0.7267 (m-80) cc_final: 0.6682 (t80) REVERT: C 262 ASN cc_start: 0.8140 (OUTLIER) cc_final: 0.7759 (p0) REVERT: D 57 MET cc_start: 0.7675 (ptp) cc_final: 0.6301 (ptp) REVERT: D 116 THR cc_start: 0.8746 (m) cc_final: 0.8471 (p) REVERT: D 185 LYS cc_start: 0.8588 (mttt) cc_final: 0.8211 (mttp) REVERT: D 195 GLN cc_start: 0.8760 (mt0) cc_final: 0.8264 (mm-40) REVERT: D 233 TYR cc_start: 0.7253 (m-80) cc_final: 0.6731 (t80) REVERT: D 262 ASN cc_start: 0.8229 (OUTLIER) cc_final: 0.7911 (p0) REVERT: E 116 THR cc_start: 0.8726 (m) cc_final: 0.8341 (p) REVERT: E 185 LYS cc_start: 0.8576 (mttt) cc_final: 0.8251 (mttp) REVERT: E 195 GLN cc_start: 0.8702 (mt0) cc_final: 0.8261 (mm-40) REVERT: E 233 TYR cc_start: 0.7231 (m-80) cc_final: 0.6739 (t80) REVERT: E 242 LYS cc_start: 0.7150 (OUTLIER) cc_final: 0.6929 (tppp) REVERT: F 2 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8197 (mt-10) REVERT: F 57 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.6355 (ptp) REVERT: F 116 THR cc_start: 0.8726 (m) cc_final: 0.8434 (p) REVERT: F 185 LYS cc_start: 0.8542 (mttt) cc_final: 0.8215 (mttm) REVERT: F 195 GLN cc_start: 0.8709 (mt0) cc_final: 0.8168 (mm110) REVERT: F 233 TYR cc_start: 0.7238 (m-80) cc_final: 0.6648 (t80) REVERT: F 238 LYS cc_start: 0.8337 (ttpp) cc_final: 0.8002 (ttpp) REVERT: F 262 ASN cc_start: 0.8044 (OUTLIER) cc_final: 0.7745 (p0) REVERT: F 378 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.8090 (tt0) REVERT: G 57 MET cc_start: 0.7735 (ptp) cc_final: 0.6511 (ptp) REVERT: G 116 THR cc_start: 0.8711 (m) cc_final: 0.8362 (p) REVERT: G 185 LYS cc_start: 0.8589 (mttt) cc_final: 0.8177 (mttp) REVERT: G 195 GLN cc_start: 0.8731 (mt0) cc_final: 0.8289 (mm-40) REVERT: G 233 TYR cc_start: 0.7258 (m-80) cc_final: 0.6874 (t80) REVERT: G 262 ASN cc_start: 0.8006 (OUTLIER) cc_final: 0.7687 (p0) outliers start: 51 outliers final: 25 residues processed: 240 average time/residue: 0.7088 time to fit residues: 192.9897 Evaluate side-chains 242 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 207 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 378 GLN Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain E residue 8 GLN Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 262 ASN Chi-restraints excluded: chain F residue 378 GLN Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 171 LYS Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 262 ASN Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain G residue 408 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 266 optimal weight: 3.9990 chunk 260 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 246 optimal weight: 0.7980 chunk 206 optimal weight: 5.9990 chunk 218 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN C 231 ASN D 231 ASN E 231 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.097472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.068630 restraints weight = 31676.471| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 2.20 r_work: 0.2662 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2559 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 23002 Z= 0.128 Angle : 0.518 6.546 31402 Z= 0.282 Chirality : 0.045 0.142 3297 Planarity : 0.004 0.030 4088 Dihedral : 4.096 15.557 3087 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.84 % Allowed : 12.70 % Favored : 85.46 % 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: 0.83 (0.15), residues: 2800 helix: 1.21 (0.23), residues: 497 sheet: 1.42 (0.15), residues: 1071 loop : -0.51 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 10 TYR 0.008 0.001 TYR A 348 PHE 0.011 0.001 PHE G 321 TRP 0.009 0.001 TRP G 359 HIS 0.003 0.001 HIS C 186 Details of bonding type rmsd covalent geometry : bond 0.00239 (22995) covalent geometry : angle 0.51857 (31388) SS BOND : bond 0.00062 ( 7) SS BOND : angle 0.19638 ( 14) hydrogen bonds : bond 0.04384 ( 840) hydrogen bonds : angle 4.41558 ( 2331) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 216 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.5969 (ttp-170) cc_final: 0.5619 (mpp-170) REVERT: A 57 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.6597 (ptp) REVERT: A 116 THR cc_start: 0.8716 (m) cc_final: 0.8361 (p) REVERT: A 185 LYS cc_start: 0.8484 (mttt) cc_final: 0.8116 (mttp) REVERT: A 195 GLN cc_start: 0.8744 (mt0) cc_final: 0.8255 (mm110) REVERT: A 233 TYR cc_start: 0.7226 (m-80) cc_final: 0.6891 (t80) REVERT: A 262 ASN cc_start: 0.7884 (OUTLIER) cc_final: 0.7542 (p0) REVERT: B 57 MET cc_start: 0.7830 (ptp) cc_final: 0.6488 (ptp) REVERT: B 116 THR cc_start: 0.8728 (m) cc_final: 0.8395 (p) REVERT: B 185 LYS cc_start: 0.8542 (mttt) cc_final: 0.8201 (mttp) REVERT: B 195 GLN cc_start: 0.8735 (mt0) cc_final: 0.8313 (mm-40) REVERT: B 233 TYR cc_start: 0.7268 (m-80) cc_final: 0.6903 (t80) REVERT: B 262 ASN cc_start: 0.8066 (OUTLIER) cc_final: 0.7703 (p0) REVERT: C 116 THR cc_start: 0.8711 (m) cc_final: 0.8382 (p) REVERT: C 185 LYS cc_start: 0.8528 (mttt) cc_final: 0.8095 (mttp) REVERT: C 195 GLN cc_start: 0.8726 (mt0) cc_final: 0.8234 (mm-40) REVERT: C 233 TYR cc_start: 0.7175 (m-80) cc_final: 0.6613 (t80) REVERT: C 242 LYS cc_start: 0.7182 (tppt) cc_final: 0.6966 (tppp) REVERT: C 262 ASN cc_start: 0.8066 (OUTLIER) cc_final: 0.7694 (p0) REVERT: D 57 MET cc_start: 0.7668 (ptp) cc_final: 0.6311 (ptp) REVERT: D 116 THR cc_start: 0.8707 (m) cc_final: 0.8400 (p) REVERT: D 185 LYS cc_start: 0.8586 (mttt) cc_final: 0.8223 (mttp) REVERT: D 195 GLN cc_start: 0.8749 (mt0) cc_final: 0.8210 (mm110) REVERT: D 233 TYR cc_start: 0.7189 (m-80) cc_final: 0.6680 (t80) REVERT: D 262 ASN cc_start: 0.8169 (OUTLIER) cc_final: 0.7861 (p0) REVERT: E 10 ARG cc_start: 0.3375 (ptt-90) cc_final: 0.3134 (ptt-90) REVERT: E 116 THR cc_start: 0.8721 (m) cc_final: 0.8300 (p) REVERT: E 185 LYS cc_start: 0.8557 (mttt) cc_final: 0.8225 (mttp) REVERT: E 195 GLN cc_start: 0.8684 (mt0) cc_final: 0.8187 (mm110) REVERT: E 233 TYR cc_start: 0.7175 (m-80) cc_final: 0.6678 (t80) REVERT: E 242 LYS cc_start: 0.7186 (OUTLIER) cc_final: 0.6970 (tppp) REVERT: E 262 ASN cc_start: 0.8120 (OUTLIER) cc_final: 0.7770 (p0) REVERT: F 2 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8194 (mt-10) REVERT: F 57 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.6341 (ptp) REVERT: F 116 THR cc_start: 0.8728 (m) cc_final: 0.8419 (p) REVERT: F 185 LYS cc_start: 0.8539 (mttt) cc_final: 0.8217 (mttm) REVERT: F 195 GLN cc_start: 0.8702 (mt0) cc_final: 0.8176 (mm110) REVERT: F 233 TYR cc_start: 0.7167 (m-80) cc_final: 0.6596 (t80) REVERT: F 238 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7948 (ttpp) REVERT: F 262 ASN cc_start: 0.7983 (OUTLIER) cc_final: 0.7690 (p0) REVERT: G 57 MET cc_start: 0.7767 (ptp) cc_final: 0.6536 (ptp) REVERT: G 116 THR cc_start: 0.8686 (m) cc_final: 0.8323 (p) REVERT: G 185 LYS cc_start: 0.8590 (mttt) cc_final: 0.8209 (mttp) REVERT: G 195 GLN cc_start: 0.8712 (mt0) cc_final: 0.8298 (mm-40) REVERT: G 233 TYR cc_start: 0.7224 (m-80) cc_final: 0.6869 (t80) REVERT: G 262 ASN cc_start: 0.7930 (OUTLIER) cc_final: 0.7612 (p0) outliers start: 44 outliers final: 21 residues processed: 238 average time/residue: 0.6844 time to fit residues: 186.2410 Evaluate side-chains 248 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 216 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain F residue 262 ASN Chi-restraints excluded: chain G residue 8 GLN Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 171 LYS Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 262 ASN Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain G residue 408 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 120 optimal weight: 6.9990 chunk 227 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 chunk 265 optimal weight: 10.0000 chunk 108 optimal weight: 0.4980 chunk 145 optimal weight: 8.9990 chunk 220 optimal weight: 4.9990 chunk 253 optimal weight: 1.9990 chunk 211 optimal weight: 7.9990 chunk 166 optimal weight: 9.9990 chunk 195 optimal weight: 4.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN B 52 ASN C 231 ASN E 52 ASN F 231 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.094448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.065488 restraints weight = 31866.999| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 2.19 r_work: 0.2596 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2492 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 23002 Z= 0.204 Angle : 0.607 6.603 31402 Z= 0.335 Chirality : 0.048 0.143 3297 Planarity : 0.005 0.034 4088 Dihedral : 4.476 16.401 3087 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.55 % Allowed : 13.07 % Favored : 85.38 % 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: 0.74 (0.15), residues: 2800 helix: 1.07 (0.23), residues: 497 sheet: 1.47 (0.15), residues: 1064 loop : -0.63 (0.16), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 24 TYR 0.010 0.002 TYR E 61 PHE 0.019 0.002 PHE A 321 TRP 0.010 0.001 TRP F 359 HIS 0.004 0.001 HIS G 186 Details of bonding type rmsd covalent geometry : bond 0.00441 (22995) covalent geometry : angle 0.60755 (31388) SS BOND : bond 0.00163 ( 7) SS BOND : angle 0.37974 ( 14) hydrogen bonds : bond 0.06117 ( 840) hydrogen bonds : angle 4.56068 ( 2331) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 216 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.5962 (ttp-170) cc_final: 0.5601 (mpp-170) REVERT: A 57 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.6629 (ptp) REVERT: A 116 THR cc_start: 0.8750 (m) cc_final: 0.8374 (p) REVERT: A 185 LYS cc_start: 0.8522 (mttt) cc_final: 0.8142 (mttp) REVERT: A 195 GLN cc_start: 0.8770 (mt0) cc_final: 0.8281 (mm110) REVERT: A 233 TYR cc_start: 0.7438 (m-80) cc_final: 0.7013 (t80) REVERT: A 262 ASN cc_start: 0.8041 (OUTLIER) cc_final: 0.7699 (p0) REVERT: B 57 MET cc_start: 0.7865 (ptp) cc_final: 0.6499 (ptp) REVERT: B 116 THR cc_start: 0.8775 (m) cc_final: 0.8418 (p) REVERT: B 185 LYS cc_start: 0.8555 (mttt) cc_final: 0.8210 (mttp) REVERT: B 195 GLN cc_start: 0.8753 (mt0) cc_final: 0.8312 (mm-40) REVERT: B 233 TYR cc_start: 0.7468 (m-80) cc_final: 0.7020 (t80) REVERT: B 262 ASN cc_start: 0.8212 (OUTLIER) cc_final: 0.7848 (p0) REVERT: C 116 THR cc_start: 0.8791 (m) cc_final: 0.8437 (p) REVERT: C 185 LYS cc_start: 0.8576 (mttt) cc_final: 0.8169 (mttp) REVERT: C 195 GLN cc_start: 0.8758 (mt0) cc_final: 0.8222 (mm110) REVERT: C 233 TYR cc_start: 0.7405 (m-80) cc_final: 0.6820 (t80) REVERT: C 242 LYS cc_start: 0.7172 (tppt) cc_final: 0.6955 (tppp) REVERT: C 262 ASN cc_start: 0.8265 (OUTLIER) cc_final: 0.7902 (p0) REVERT: D 57 MET cc_start: 0.7678 (ptp) cc_final: 0.6320 (ptp) REVERT: D 116 THR cc_start: 0.8794 (m) cc_final: 0.8470 (p) REVERT: D 185 LYS cc_start: 0.8611 (mttt) cc_final: 0.8239 (mttp) REVERT: D 195 GLN cc_start: 0.8776 (mt0) cc_final: 0.8213 (mm110) REVERT: D 233 TYR cc_start: 0.7376 (m-80) cc_final: 0.6757 (t80) REVERT: D 262 ASN cc_start: 0.8294 (OUTLIER) cc_final: 0.7959 (p0) REVERT: E 10 ARG cc_start: 0.3458 (ptt-90) cc_final: 0.3162 (ptt-90) REVERT: E 116 THR cc_start: 0.8739 (m) cc_final: 0.8329 (p) REVERT: E 185 LYS cc_start: 0.8595 (mttt) cc_final: 0.8276 (mttp) REVERT: E 195 GLN cc_start: 0.8697 (mt0) cc_final: 0.8260 (mm-40) REVERT: E 233 TYR cc_start: 0.7358 (m-80) cc_final: 0.6828 (t80) REVERT: E 242 LYS cc_start: 0.7193 (OUTLIER) cc_final: 0.6973 (tppp) REVERT: F 2 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8229 (mt-10) REVERT: F 57 MET cc_start: 0.7849 (ptp) cc_final: 0.6405 (ptp) REVERT: F 185 LYS cc_start: 0.8556 (mttt) cc_final: 0.8234 (mttm) REVERT: F 195 GLN cc_start: 0.8727 (mt0) cc_final: 0.8175 (mm110) REVERT: F 233 TYR cc_start: 0.7369 (m-80) cc_final: 0.6753 (t80) REVERT: F 238 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8035 (ttpp) REVERT: F 262 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7871 (p0) REVERT: G 57 MET cc_start: 0.7760 (ptp) cc_final: 0.6518 (ptp) REVERT: G 116 THR cc_start: 0.8735 (m) cc_final: 0.8356 (p) REVERT: G 185 LYS cc_start: 0.8609 (mttt) cc_final: 0.8191 (mttp) REVERT: G 195 GLN cc_start: 0.8726 (mt0) cc_final: 0.8288 (mm-40) REVERT: G 233 TYR cc_start: 0.7390 (m-80) cc_final: 0.6983 (t80) outliers start: 37 outliers final: 24 residues processed: 240 average time/residue: 0.6917 time to fit residues: 188.9299 Evaluate side-chains 244 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 212 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain F residue 256 SER Chi-restraints excluded: chain F residue 262 ASN Chi-restraints excluded: chain G residue 8 GLN Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 171 LYS Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain G residue 408 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 259 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 187 optimal weight: 0.5980 chunk 64 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 172 optimal weight: 9.9990 chunk 193 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 52 ASN G 52 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.097319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.068459 restraints weight = 31807.623| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 2.20 r_work: 0.2655 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2552 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23002 Z= 0.131 Angle : 0.526 6.454 31402 Z= 0.287 Chirality : 0.045 0.144 3297 Planarity : 0.004 0.030 4088 Dihedral : 4.136 15.850 3087 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.50 % Allowed : 13.07 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.81 (0.15), residues: 2800 helix: 1.16 (0.23), residues: 497 sheet: 1.42 (0.15), residues: 1071 loop : -0.52 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 10 TYR 0.008 0.001 TYR A 348 PHE 0.010 0.001 PHE G 321 TRP 0.009 0.001 TRP A 265 HIS 0.003 0.001 HIS C 186 Details of bonding type rmsd covalent geometry : bond 0.00244 (22995) covalent geometry : angle 0.52596 (31388) SS BOND : bond 0.00082 ( 7) SS BOND : angle 0.24491 ( 14) hydrogen bonds : bond 0.04371 ( 840) hydrogen bonds : angle 4.46314 ( 2331) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10889.67 seconds wall clock time: 185 minutes 28.86 seconds (11128.86 seconds total)