Starting phenix.real_space_refine on Thu Aug 6 10:22:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vh4_65055/08_2026/9vh4_65055.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vh4_65055/08_2026/9vh4_65055.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vh4_65055/08_2026/9vh4_65055.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vh4_65055/08_2026/9vh4_65055.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vh4_65055/08_2026/9vh4_65055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vh4_65055/08_2026/9vh4_65055.map" } resolution = 2.8 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= 0.001 sd= 0.029 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 72 5.16 5 C 9063 2.51 5 N 2496 2.21 5 O 2775 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14406 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2542 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "B" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1340 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 1, 'TRANS': 163} Chain: "C" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 920 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Restraints were copied for chains: D, G, E, H, F, I Time building chain proxies: 3.23, per 1000 atoms: 0.22 Number of scatterers: 14406 At special positions: 0 Unit cell: (123.69, 117.18, 144.15, 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 72 16.00 O 2775 8.00 N 2496 7.00 C 9063 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS B 480 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 72 " - pdb=" SG CYS A 84 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 319 " distance=2.03 Simple disulfide: pdb=" SG CYS B 487 " - pdb=" SG CYS B 491 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS E 480 " distance=2.01 Simple disulfide: pdb=" SG CYS G 21 " - pdb=" SG CYS H 480 " distance=2.01 Simple disulfide: pdb=" SG CYS D 59 " - pdb=" SG CYS D 291 " distance=2.03 Simple disulfide: pdb=" SG CYS G 59 " - pdb=" SG CYS G 291 " distance=2.03 Simple disulfide: pdb=" SG CYS D 72 " - pdb=" SG CYS D 84 " distance=2.02 Simple disulfide: pdb=" SG CYS G 72 " - pdb=" SG CYS G 84 " distance=2.03 Simple disulfide: pdb=" SG CYS D 107 " - pdb=" SG CYS D 152 " distance=2.03 Simple disulfide: pdb=" SG CYS G 107 " - pdb=" SG CYS G 152 " distance=2.03 Simple disulfide: pdb=" SG CYS D 295 " - pdb=" SG CYS D 319 " distance=2.03 Simple disulfide: pdb=" SG CYS G 295 " - pdb=" SG CYS G 319 " distance=2.03 Simple disulfide: pdb=" SG CYS E 487 " - pdb=" SG CYS E 491 " distance=2.03 Simple disulfide: pdb=" SG CYS H 487 " - pdb=" SG CYS H 491 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " 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: 1.16 Conformation dependent library (CDL) restraints added in 803.3 milliseconds 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3348 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 42 sheets defined 22.6% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 73 through 80 Processing helix chain 'A' and resid 114 through 123 Processing helix chain 'A' and resid 200 through 208 Processing helix chain 'B' and resid 380 through 402 removed outlier: 3.636A pdb=" N MET B 402 " --> pdb=" O VAL B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 470 Processing helix chain 'B' and resid 488 through 497 Processing helix chain 'B' and resid 505 through 514 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 74 through 76 No H-bonds generated for 'chain 'I' and resid 74 through 76' Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'D' and resid 73 through 80 Processing helix chain 'D' and resid 114 through 123 Processing helix chain 'D' and resid 200 through 208 Processing helix chain 'G' and resid 73 through 80 Processing helix chain 'G' and resid 114 through 123 Processing helix chain 'G' and resid 200 through 208 Processing helix chain 'E' and resid 380 through 402 removed outlier: 3.636A pdb=" N MET E 402 " --> pdb=" O VAL E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 470 Processing helix chain 'E' and resid 488 through 497 Processing helix chain 'E' and resid 505 through 514 Processing helix chain 'H' and resid 380 through 402 removed outlier: 3.636A pdb=" N MET H 402 " --> pdb=" O VAL H 398 " (cutoff:3.500A) Processing helix chain 'H' and resid 417 through 470 Processing helix chain 'H' and resid 488 through 497 Processing helix chain 'H' and resid 505 through 514 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 removed outlier: 3.580A pdb=" N ASN B 371 " --> pdb=" O GLY B 374 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 24 removed outlier: 3.505A pdb=" N HIS B 368 " --> pdb=" O CYS A 21 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 33 removed outlier: 4.099A pdb=" N ASP A 31 " --> pdb=" O VAL A 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 46 through 48 Processing sheet with id=AA5, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AA6, first strand: chain 'A' and resid 67 through 68 removed outlier: 6.603A pdb=" N LEU A 67 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 125 through 127 removed outlier: 3.619A pdb=" N SER A 127 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TYR A 269 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU A 192 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU A 188 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N LEU A 192 " --> pdb=" O PRO A 267 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 130 through 132 removed outlier: 6.712A pdb=" N TYR A 269 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU A 192 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU A 188 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 149 through 154 removed outlier: 4.541A pdb=" N CYS A 152 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 177 through 182 Processing sheet with id=AB2, first strand: chain 'A' and resid 301 through 302 removed outlier: 3.685A pdb=" N CYS A 295 " --> pdb=" O ILE A 302 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.636A pdb=" N SER C 71 " --> pdb=" O TYR C 80 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.603A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N SER C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N MET C 34 " --> pdb=" O SER C 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.603A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N SER C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N MET C 34 " --> pdb=" O SER C 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.636A pdb=" N SER F 71 " --> pdb=" O TYR F 80 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.603A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N SER F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N MET F 34 " --> pdb=" O SER F 50 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.603A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N SER F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N MET F 34 " --> pdb=" O SER F 50 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.636A pdb=" N SER I 71 " --> pdb=" O TYR I 80 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.603A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N SER I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N MET I 34 " --> pdb=" O SER I 50 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.603A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N SER I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N MET I 34 " --> pdb=" O SER I 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 23 through 24 removed outlier: 3.516A pdb=" N GLY E 366 " --> pdb=" O GLY D 23 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN E 371 " --> pdb=" O GLY E 374 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 23 through 24 removed outlier: 3.516A pdb=" N GLY E 366 " --> pdb=" O GLY D 23 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS E 368 " --> pdb=" O CYS D 21 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 31 through 33 removed outlier: 4.100A pdb=" N ASP D 31 " --> pdb=" O VAL D 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 46 through 48 Processing sheet with id=AC7, first strand: chain 'D' and resid 50 through 51 Processing sheet with id=AC8, first strand: chain 'D' and resid 67 through 68 removed outlier: 6.604A pdb=" N LEU D 67 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 125 through 127 removed outlier: 3.619A pdb=" N SER D 127 " --> pdb=" O SER D 274 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TYR D 269 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU D 192 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU D 188 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N LEU D 192 " --> pdb=" O PRO D 267 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 130 through 132 removed outlier: 6.712A pdb=" N TYR D 269 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU D 192 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU D 188 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 149 through 154 removed outlier: 4.541A pdb=" N CYS D 152 " --> pdb=" O SER D 159 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 177 through 182 Processing sheet with id=AD4, first strand: chain 'D' and resid 301 through 302 removed outlier: 3.684A pdb=" N CYS D 295 " --> pdb=" O ILE D 302 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 23 through 24 removed outlier: 3.509A pdb=" N GLY H 366 " --> pdb=" O GLY G 23 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN H 371 " --> pdb=" O GLY H 374 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 23 through 24 removed outlier: 3.509A pdb=" N GLY H 366 " --> pdb=" O GLY G 23 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS H 368 " --> pdb=" O CYS G 21 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 31 through 33 removed outlier: 4.099A pdb=" N ASP G 31 " --> pdb=" O VAL G 43 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 46 through 48 Processing sheet with id=AD9, first strand: chain 'G' and resid 50 through 51 Processing sheet with id=AE1, first strand: chain 'G' and resid 67 through 68 removed outlier: 6.604A pdb=" N LEU G 67 " --> pdb=" O VAL G 97 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 125 through 127 removed outlier: 3.619A pdb=" N SER G 127 " --> pdb=" O SER G 274 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TYR G 269 " --> pdb=" O LEU G 192 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU G 192 " --> pdb=" O TYR G 269 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU G 188 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N LEU G 192 " --> pdb=" O PRO G 267 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 130 through 132 removed outlier: 6.712A pdb=" N TYR G 269 " --> pdb=" O LEU G 192 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU G 192 " --> pdb=" O TYR G 269 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU G 188 " --> pdb=" O LEU G 273 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 149 through 154 removed outlier: 4.541A pdb=" N CYS G 152 " --> pdb=" O SER G 159 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 177 through 182 Processing sheet with id=AE6, first strand: chain 'G' and resid 301 through 302 removed outlier: 3.685A pdb=" N CYS G 295 " --> pdb=" O ILE G 302 " (cutoff:3.500A) 620 hydrogen bonds defined for protein. 1662 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4785 1.34 - 1.46: 3453 1.46 - 1.58: 6396 1.58 - 1.70: 0 1.70 - 1.82: 102 Bond restraints: 14736 Sorted by residual: bond pdb=" C LYS D 62 " pdb=" N GLY D 63 " ideal model delta sigma weight residual 1.333 1.316 0.016 1.36e-02 5.41e+03 1.44e+00 bond pdb=" C LYS G 62 " pdb=" N GLY G 63 " ideal model delta sigma weight residual 1.333 1.316 0.016 1.36e-02 5.41e+03 1.40e+00 bond pdb=" C LYS A 62 " pdb=" N GLY A 63 " ideal model delta sigma weight residual 1.333 1.317 0.016 1.36e-02 5.41e+03 1.36e+00 bond pdb=" CA GLY I 101 " pdb=" C GLY I 101 " ideal model delta sigma weight residual 1.514 1.498 0.016 1.41e-02 5.03e+03 1.33e+00 bond pdb=" CA GLY C 101 " pdb=" C GLY C 101 " ideal model delta sigma weight residual 1.514 1.498 0.016 1.41e-02 5.03e+03 1.26e+00 ... (remaining 14731 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 19456 1.77 - 3.53: 403 3.53 - 5.30: 70 5.30 - 7.06: 15 7.06 - 8.83: 6 Bond angle restraints: 19950 Sorted by residual: angle pdb=" N VAL I 12 " pdb=" CA VAL I 12 " pdb=" C VAL I 12 " ideal model delta sigma weight residual 113.71 110.57 3.14 9.50e-01 1.11e+00 1.09e+01 angle pdb=" C TYR G 208 " pdb=" N GLN G 209 " pdb=" CA GLN G 209 " ideal model delta sigma weight residual 122.08 126.92 -4.84 1.47e+00 4.63e-01 1.09e+01 angle pdb=" C TYR A 208 " pdb=" N GLN A 209 " pdb=" CA GLN A 209 " ideal model delta sigma weight residual 122.08 126.92 -4.84 1.47e+00 4.63e-01 1.08e+01 angle pdb=" N VAL F 12 " pdb=" CA VAL F 12 " pdb=" C VAL F 12 " ideal model delta sigma weight residual 113.71 110.59 3.12 9.50e-01 1.11e+00 1.08e+01 angle pdb=" N VAL C 12 " pdb=" CA VAL C 12 " pdb=" C VAL C 12 " ideal model delta sigma weight residual 113.71 110.60 3.11 9.50e-01 1.11e+00 1.08e+01 ... (remaining 19945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 7573 16.75 - 33.49: 942 33.49 - 50.24: 239 50.24 - 66.99: 69 66.99 - 83.73: 21 Dihedral angle restraints: 8844 sinusoidal: 3603 harmonic: 5241 Sorted by residual: dihedral pdb=" CB CYS D 59 " pdb=" SG CYS D 59 " pdb=" SG CYS D 291 " pdb=" CB CYS D 291 " ideal model delta sinusoidal sigma weight residual -86.00 -115.30 29.30 1 1.00e+01 1.00e-02 1.23e+01 dihedral pdb=" CB CYS A 59 " pdb=" SG CYS A 59 " pdb=" SG CYS A 291 " pdb=" CB CYS A 291 " ideal model delta sinusoidal sigma weight residual -86.00 -115.29 29.29 1 1.00e+01 1.00e-02 1.23e+01 dihedral pdb=" CB CYS G 59 " pdb=" SG CYS G 59 " pdb=" SG CYS G 291 " pdb=" CB CYS G 291 " ideal model delta sinusoidal sigma weight residual -86.00 -115.27 29.27 1 1.00e+01 1.00e-02 1.23e+01 ... (remaining 8841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1234 0.030 - 0.059: 564 0.059 - 0.089: 172 0.089 - 0.119: 134 0.119 - 0.148: 14 Chirality restraints: 2118 Sorted by residual: chirality pdb=" CA GLN D 209 " pdb=" N GLN D 209 " pdb=" C GLN D 209 " pdb=" CB GLN D 209 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA GLN A 209 " pdb=" N GLN A 209 " pdb=" C GLN A 209 " pdb=" CB GLN A 209 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA GLN G 209 " pdb=" N GLN G 209 " pdb=" C GLN G 209 " pdb=" CB GLN G 209 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.26e-01 ... (remaining 2115 not shown) Planarity restraints: 2616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN E 478 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" C ASN E 478 " -0.033 2.00e-02 2.50e+03 pdb=" O ASN E 478 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY E 479 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 478 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" C ASN B 478 " -0.033 2.00e-02 2.50e+03 pdb=" O ASN B 478 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY B 479 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 87 " -0.031 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO F 88 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO F 88 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 88 " -0.026 5.00e-02 4.00e+02 ... (remaining 2613 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.89: 15 1.89 - 2.64: 225 2.64 - 3.39: 19273 3.39 - 4.15: 37010 4.15 - 4.90: 67204 Nonbonded interactions: 123727 Sorted by model distance: nonbonded pdb=" ND2 ASN A 221 " pdb=" NZ LYS H 415 " model vdw 1.136 3.200 nonbonded pdb=" NZ LYS B 415 " pdb=" ND2 ASN D 221 " model vdw 1.149 3.200 nonbonded pdb=" CE MET B 420 " pdb=" CE MET E 420 " model vdw 1.160 3.880 nonbonded pdb=" ND2 ASN G 221 " pdb=" NZ LYS E 415 " model vdw 1.165 3.200 nonbonded pdb=" CE MET B 420 " pdb=" CE MET H 420 " model vdw 1.182 3.880 ... (remaining 123722 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 14.270 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:6.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 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 0.036 14757 Z= 0.185 Angle : 0.651 8.831 19992 Z= 0.347 Chirality : 0.043 0.148 2118 Planarity : 0.005 0.056 2616 Dihedral : 16.515 83.732 5433 Min Nonbonded Distance : 1.136 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.51 % Allowed : 24.37 % Favored : 75.13 % 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: -0.09 (0.19), residues: 1800 helix: 2.66 (0.26), residues: 354 sheet: -1.07 (0.26), residues: 414 loop : -0.56 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 91 TYR 0.018 0.001 TYR E 367 PHE 0.013 0.001 PHE G 128 TRP 0.006 0.001 TRP C 109 HIS 0.003 0.001 HIS G 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (14736) covalent geometry : angle 0.65061 / 0.35 (19950) SS BOND : bond 0.00768 / 0.52 ( 21) SS BOND : angle 0.95554 / 0.64 ( 42) hydrogen bonds : bond 0.18022 / 12.18 ( 574) hydrogen bonds : angle 8.12636 / 5.82 ( 1662) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 390 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 370 GLN cc_start: 0.8290 (tm-30) cc_final: 0.7805 (pp30) REVERT: G 52 ASP cc_start: 0.8699 (p0) cc_final: 0.8496 (p0) REVERT: E 370 GLN cc_start: 0.8277 (tm-30) cc_final: 0.7833 (pp30) REVERT: H 370 GLN cc_start: 0.8259 (tm-30) cc_final: 0.7779 (pp30) outliers start: 8 outliers final: 3 residues processed: 395 average time/residue: 0.5622 time to fit residues: 242.3898 Evaluate side-chains 272 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 269 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain G residue 238 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 221 ASN B 424 ASN ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 GLN D 221 ASN G 221 ASN E 424 ASN ** E 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 424 ASN ** H 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.086596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.060631 restraints weight = 36207.224| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.19 r_work: 0.2933 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14757 Z= 0.155 Angle : 0.635 8.900 19992 Z= 0.324 Chirality : 0.044 0.176 2118 Planarity : 0.005 0.052 2616 Dihedral : 5.809 116.879 1974 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.91 % Allowed : 23.74 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.19), residues: 1800 helix: 2.61 (0.26), residues: 357 sheet: -0.90 (0.26), residues: 408 loop : -0.66 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 57 TYR 0.026 0.002 TYR E 502 PHE 0.014 0.002 PHE I 68 TRP 0.006 0.001 TRP H 435 HIS 0.002 0.001 HIS H 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (14736) covalent geometry : angle 0.63372 / 0.32 (19950) SS BOND : bond 0.00367 / 0.27 ( 21) SS BOND : angle 1.05630 / 0.72 ( 42) hydrogen bonds : bond 0.04388 / 2.93 ( 574) hydrogen bonds : angle 5.84286 / 4.10 ( 1662) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 300 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8446 (mp0) cc_final: 0.8055 (mp0) REVERT: A 188 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8508 (pt0) REVERT: B 361 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.8872 (pp) REVERT: B 429 ASP cc_start: 0.8775 (m-30) cc_final: 0.8506 (m-30) REVERT: B 448 GLU cc_start: 0.8597 (tp30) cc_final: 0.8374 (mm-30) REVERT: C 19 ARG cc_start: 0.8742 (ttt90) cc_final: 0.8460 (ttt90) REVERT: C 60 TYR cc_start: 0.8489 (m-80) cc_final: 0.7930 (m-80) REVERT: C 67 ARG cc_start: 0.8966 (mtm-85) cc_final: 0.8441 (ptm-80) REVERT: F 100 ARG cc_start: 0.8846 (ttm170) cc_final: 0.8548 (ttm170) REVERT: I 38 ARG cc_start: 0.8661 (ptt-90) cc_final: 0.8319 (ptt180) REVERT: I 77 ASN cc_start: 0.9180 (m-40) cc_final: 0.8972 (t0) REVERT: D 38 GLU cc_start: 0.8371 (mp0) cc_final: 0.7991 (mp0) REVERT: D 188 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8402 (pt0) REVERT: G 38 GLU cc_start: 0.8437 (mp0) cc_final: 0.8168 (mp0) REVERT: G 52 ASP cc_start: 0.8929 (OUTLIER) cc_final: 0.8699 (p0) REVERT: G 188 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8475 (pt0) REVERT: E 370 GLN cc_start: 0.8700 (tm-30) cc_final: 0.7669 (pp30) REVERT: E 448 GLU cc_start: 0.8639 (tp30) cc_final: 0.8401 (mm-30) REVERT: E 501 ASP cc_start: 0.8907 (t0) cc_final: 0.8702 (OUTLIER) REVERT: H 358 THR cc_start: 0.9168 (p) cc_final: 0.8887 (m) REVERT: H 361 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.8905 (pp) REVERT: H 370 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8441 (tm-30) REVERT: H 381 GLN cc_start: 0.9221 (mt0) cc_final: 0.8858 (mm-40) REVERT: H 448 GLU cc_start: 0.8663 (tp30) cc_final: 0.8406 (mm-30) outliers start: 62 outliers final: 20 residues processed: 338 average time/residue: 0.4892 time to fit residues: 183.3388 Evaluate side-chains 300 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 275 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 367 TYR Chi-restraints excluded: chain H residue 400 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 109 optimal weight: 1.9990 chunk 122 optimal weight: 0.0770 chunk 8 optimal weight: 5.9990 chunk 167 optimal weight: 3.9990 chunk 118 optimal weight: 0.0670 chunk 126 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 161 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 148 optimal weight: 0.5980 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN I 35 ASN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN ** E 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 386 ASN ** H 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.087113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.061055 restraints weight = 36406.058| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.21 r_work: 0.2939 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14757 Z= 0.126 Angle : 0.584 7.632 19992 Z= 0.298 Chirality : 0.043 0.156 2118 Planarity : 0.004 0.052 2616 Dihedral : 4.341 59.764 1970 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.54 % Allowed : 24.43 % Favored : 72.03 % 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: -0.06 (0.19), residues: 1800 helix: 2.60 (0.26), residues: 363 sheet: -0.79 (0.26), residues: 408 loop : -0.68 (0.17), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 57 TYR 0.027 0.002 TYR H 502 PHE 0.022 0.001 PHE I 68 TRP 0.005 0.001 TRP E 435 HIS 0.002 0.000 HIS G 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (14736) covalent geometry : angle 0.58295 / 0.30 (19950) SS BOND : bond 0.00309 / 0.22 ( 21) SS BOND : angle 0.94687 / 0.66 ( 42) hydrogen bonds : bond 0.03716 / 2.49 ( 574) hydrogen bonds : angle 5.39575 / 3.77 ( 1662) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 293 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8464 (mp0) cc_final: 0.8074 (mp0) REVERT: A 188 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8499 (pt0) REVERT: B 361 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8685 (pp) REVERT: B 381 GLN cc_start: 0.9240 (mt0) cc_final: 0.8959 (mm-40) REVERT: B 448 GLU cc_start: 0.8675 (tp30) cc_final: 0.8452 (mm-30) REVERT: C 60 TYR cc_start: 0.8497 (m-80) cc_final: 0.7864 (m-80) REVERT: C 67 ARG cc_start: 0.8966 (mtm-85) cc_final: 0.8416 (ptm-80) REVERT: C 76 LYS cc_start: 0.9398 (mtpt) cc_final: 0.9138 (mtpp) REVERT: F 18 LEU cc_start: 0.8981 (tp) cc_final: 0.8736 (tt) REVERT: F 19 ARG cc_start: 0.9095 (ttt90) cc_final: 0.8866 (ttt90) REVERT: D 38 GLU cc_start: 0.8362 (mp0) cc_final: 0.8114 (mp0) REVERT: D 188 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8350 (pt0) REVERT: D 220 SER cc_start: 0.8941 (m) cc_final: 0.8730 (p) REVERT: G 52 ASP cc_start: 0.8901 (OUTLIER) cc_final: 0.8678 (p0) REVERT: E 381 GLN cc_start: 0.9271 (mt0) cc_final: 0.9026 (mm-40) REVERT: E 501 ASP cc_start: 0.8909 (t0) cc_final: 0.8618 (t0) REVERT: H 358 THR cc_start: 0.9178 (OUTLIER) cc_final: 0.8924 (m) REVERT: H 361 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8705 (pp) REVERT: H 370 GLN cc_start: 0.8604 (tm-30) cc_final: 0.8381 (tm-30) REVERT: H 381 GLN cc_start: 0.9238 (mt0) cc_final: 0.8987 (mm-40) REVERT: H 448 GLU cc_start: 0.8691 (tp30) cc_final: 0.8451 (mm-30) outliers start: 56 outliers final: 19 residues processed: 328 average time/residue: 0.5014 time to fit residues: 182.5167 Evaluate side-chains 298 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 273 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 400 GLU Chi-restraints excluded: chain H residue 441 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 154 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 126 optimal weight: 0.0970 chunk 99 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 385 GLN ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 GLN ** E 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 385 GLN ** H 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.087276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.061162 restraints weight = 36414.569| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.22 r_work: 0.2944 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14757 Z= 0.124 Angle : 0.578 9.701 19992 Z= 0.293 Chirality : 0.043 0.144 2118 Planarity : 0.005 0.053 2616 Dihedral : 4.070 14.448 1968 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.71 % Allowed : 25.44 % Favored : 71.84 % 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: 0.03 (0.19), residues: 1800 helix: 2.58 (0.26), residues: 369 sheet: -0.64 (0.25), residues: 429 loop : -0.64 (0.17), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 513 TYR 0.019 0.001 TYR I 94 PHE 0.018 0.001 PHE I 68 TRP 0.005 0.001 TRP H 435 HIS 0.002 0.000 HIS G 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (14736) covalent geometry : angle 0.57662 / 0.29 (19950) SS BOND : bond 0.00308 / 0.22 ( 21) SS BOND : angle 0.93766 / 0.64 ( 42) hydrogen bonds : bond 0.03493 / 2.33 ( 574) hydrogen bonds : angle 5.17117 / 3.60 ( 1662) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 289 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8473 (mp0) cc_final: 0.8085 (mp0) REVERT: A 188 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8538 (pt0) REVERT: B 361 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8550 (pp) REVERT: B 381 GLN cc_start: 0.9238 (mt0) cc_final: 0.8962 (mm-40) REVERT: B 406 PHE cc_start: 0.8966 (m-80) cc_final: 0.8762 (m-80) REVERT: B 448 GLU cc_start: 0.8702 (tp30) cc_final: 0.8486 (mm-30) REVERT: C 38 ARG cc_start: 0.8302 (ptt-90) cc_final: 0.8013 (ptt-90) REVERT: C 76 LYS cc_start: 0.9396 (mtpt) cc_final: 0.9133 (mtpp) REVERT: F 46 GLU cc_start: 0.8479 (pt0) cc_final: 0.8125 (pm20) REVERT: I 46 GLU cc_start: 0.8429 (pt0) cc_final: 0.8079 (pm20) REVERT: D 38 GLU cc_start: 0.8383 (mp0) cc_final: 0.8104 (mp0) REVERT: D 188 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8373 (pt0) REVERT: G 38 GLU cc_start: 0.8440 (mp0) cc_final: 0.8219 (mp0) REVERT: G 52 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.8661 (p0) REVERT: E 360 MET cc_start: 0.8878 (ttp) cc_final: 0.8598 (ptm) REVERT: E 381 GLN cc_start: 0.9244 (mt0) cc_final: 0.9015 (mm-40) REVERT: E 501 ASP cc_start: 0.8919 (t0) cc_final: 0.8610 (t0) REVERT: H 358 THR cc_start: 0.9182 (OUTLIER) cc_final: 0.8944 (m) REVERT: H 361 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8624 (pp) REVERT: H 370 GLN cc_start: 0.8612 (tm-30) cc_final: 0.8380 (tm-30) REVERT: H 381 GLN cc_start: 0.9226 (mt0) cc_final: 0.8994 (mm-40) REVERT: H 448 GLU cc_start: 0.8696 (tp30) cc_final: 0.8428 (mm-30) outliers start: 43 outliers final: 20 residues processed: 312 average time/residue: 0.5422 time to fit residues: 186.8441 Evaluate side-chains 300 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 274 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 400 GLU Chi-restraints excluded: chain H residue 441 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 4 optimal weight: 0.0770 chunk 46 optimal weight: 6.9990 chunk 142 optimal weight: 0.2980 chunk 60 optimal weight: 20.0000 chunk 98 optimal weight: 0.6980 chunk 131 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 118 optimal weight: 0.1980 chunk 42 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 414 ASN ** H 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.087631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.061628 restraints weight = 36363.203| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.20 r_work: 0.2957 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14757 Z= 0.119 Angle : 0.574 9.708 19992 Z= 0.291 Chirality : 0.043 0.156 2118 Planarity : 0.005 0.053 2616 Dihedral : 4.042 14.368 1968 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.09 % Allowed : 25.76 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.08 (0.19), residues: 1800 helix: 2.60 (0.26), residues: 369 sheet: -0.55 (0.26), residues: 408 loop : -0.63 (0.17), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 513 TYR 0.021 0.001 TYR F 94 PHE 0.018 0.001 PHE B 481 TRP 0.004 0.001 TRP I 109 HIS 0.002 0.000 HIS H 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (14736) covalent geometry : angle 0.57313 / 0.29 (19950) SS BOND : bond 0.00320 / 0.21 ( 21) SS BOND : angle 0.89675 / 0.62 ( 42) hydrogen bonds : bond 0.03344 / 2.23 ( 574) hydrogen bonds : angle 5.01710 / 3.49 ( 1662) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 285 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8521 (mp0) cc_final: 0.8124 (mp0) REVERT: B 361 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8538 (pp) REVERT: B 381 GLN cc_start: 0.9213 (mt0) cc_final: 0.8964 (mm-40) REVERT: B 406 PHE cc_start: 0.8969 (m-80) cc_final: 0.8766 (m-80) REVERT: B 463 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8512 (mm-30) REVERT: B 474 LYS cc_start: 0.9335 (OUTLIER) cc_final: 0.9127 (ttpt) REVERT: C 3 LYS cc_start: 0.9443 (ptmm) cc_final: 0.8307 (ptmm) REVERT: C 38 ARG cc_start: 0.8174 (ptt-90) cc_final: 0.7952 (ptt-90) REVERT: C 67 ARG cc_start: 0.8890 (mtm-85) cc_final: 0.8322 (ptm-80) REVERT: C 76 LYS cc_start: 0.9388 (mtpt) cc_final: 0.9119 (mtpp) REVERT: F 46 GLU cc_start: 0.8504 (pt0) cc_final: 0.8185 (pm20) REVERT: F 68 PHE cc_start: 0.8193 (m-10) cc_final: 0.7412 (m-10) REVERT: F 73 ASP cc_start: 0.8423 (t0) cc_final: 0.7813 (t0) REVERT: I 46 GLU cc_start: 0.8508 (pt0) cc_final: 0.8083 (pm20) REVERT: D 38 GLU cc_start: 0.8454 (mp0) cc_final: 0.8088 (mp0) REVERT: G 38 GLU cc_start: 0.8464 (mp0) cc_final: 0.8227 (mp0) REVERT: G 52 ASP cc_start: 0.8891 (OUTLIER) cc_final: 0.8659 (p0) REVERT: E 360 MET cc_start: 0.8864 (ttp) cc_final: 0.8587 (ptm) REVERT: E 381 GLN cc_start: 0.9245 (mt0) cc_final: 0.9030 (mm-40) REVERT: E 501 ASP cc_start: 0.8946 (t0) cc_final: 0.8667 (t0) REVERT: H 358 THR cc_start: 0.9174 (OUTLIER) cc_final: 0.8950 (m) REVERT: H 361 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8620 (pp) REVERT: H 370 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8308 (tm-30) REVERT: H 381 GLN cc_start: 0.9241 (mt0) cc_final: 0.9019 (mm-40) REVERT: H 448 GLU cc_start: 0.8646 (tp30) cc_final: 0.8425 (mm-30) outliers start: 49 outliers final: 26 residues processed: 312 average time/residue: 0.4803 time to fit residues: 166.1281 Evaluate side-chains 294 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 263 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 474 LYS Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 505 TYR Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 400 GLU Chi-restraints excluded: chain H residue 474 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 125 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 137 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 141 optimal weight: 0.0570 chunk 173 optimal weight: 4.9990 overall best weight: 1.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.084817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.058444 restraints weight = 36513.736| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.19 r_work: 0.2880 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14757 Z= 0.209 Angle : 0.610 10.107 19992 Z= 0.310 Chirality : 0.045 0.152 2118 Planarity : 0.005 0.055 2616 Dihedral : 4.175 18.271 1968 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.54 % Allowed : 25.38 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.15 (0.19), residues: 1800 helix: 2.75 (0.26), residues: 363 sheet: -0.47 (0.25), residues: 459 loop : -0.62 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 57 TYR 0.015 0.002 TYR E 367 PHE 0.020 0.002 PHE I 68 TRP 0.007 0.001 TRP G 77 HIS 0.004 0.001 HIS G 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 (14736) covalent geometry : angle 0.60865 / 0.31 (19950) SS BOND : bond 0.00393 / 0.28 ( 21) SS BOND : angle 1.07949 / 0.73 ( 42) hydrogen bonds : bond 0.03451 / 2.29 ( 574) hydrogen bonds : angle 5.07913 / 3.53 ( 1662) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 275 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 361 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8530 (pp) REVERT: B 381 GLN cc_start: 0.9192 (mt0) cc_final: 0.8944 (mm-40) REVERT: C 38 ARG cc_start: 0.8252 (ptt-90) cc_final: 0.7696 (ptt-90) REVERT: C 68 PHE cc_start: 0.8261 (m-10) cc_final: 0.7483 (m-10) REVERT: C 76 LYS cc_start: 0.9394 (mtpt) cc_final: 0.9142 (mtpp) REVERT: F 46 GLU cc_start: 0.8454 (pt0) cc_final: 0.8103 (pm20) REVERT: F 73 ASP cc_start: 0.8474 (t0) cc_final: 0.7787 (t0) REVERT: F 83 MET cc_start: 0.8190 (mmm) cc_final: 0.7672 (mmm) REVERT: F 87 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8492 (ptpp) REVERT: F 102 LEU cc_start: 0.8783 (mt) cc_final: 0.8539 (mp) REVERT: F 103 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8712 (mt-10) REVERT: I 38 ARG cc_start: 0.8552 (ptt-90) cc_final: 0.7897 (ptt180) REVERT: I 46 GLU cc_start: 0.8400 (pt0) cc_final: 0.7961 (pm20) REVERT: I 68 PHE cc_start: 0.7842 (m-10) cc_final: 0.7462 (m-10) REVERT: I 80 TYR cc_start: 0.7983 (m-80) cc_final: 0.7761 (m-80) REVERT: I 87 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8656 (ptpp) REVERT: D 164 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8653 (pp) REVERT: G 52 ASP cc_start: 0.8983 (OUTLIER) cc_final: 0.8763 (p0) REVERT: E 360 MET cc_start: 0.8929 (ttp) cc_final: 0.8687 (ptm) REVERT: E 381 GLN cc_start: 0.9234 (mt0) cc_final: 0.9007 (mm-40) REVERT: E 501 ASP cc_start: 0.8949 (t0) cc_final: 0.8667 (t0) REVERT: H 358 THR cc_start: 0.9217 (OUTLIER) cc_final: 0.8990 (m) REVERT: H 361 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8496 (pp) REVERT: H 362 ASP cc_start: 0.8753 (p0) cc_final: 0.7977 (t0) REVERT: H 370 GLN cc_start: 0.8580 (tm-30) cc_final: 0.8283 (tm-30) REVERT: H 381 GLN cc_start: 0.9241 (mt0) cc_final: 0.8967 (mm-40) REVERT: H 417 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8617 (mt-10) REVERT: H 449 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.8771 (mtp-110) REVERT: H 513 ARG cc_start: 0.8856 (ttp-110) cc_final: 0.8620 (ttm110) outliers start: 56 outliers final: 34 residues processed: 298 average time/residue: 0.4617 time to fit residues: 152.6634 Evaluate side-chains 306 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 264 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 491 CYS Chi-restraints excluded: chain E residue 505 TYR Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 400 GLU Chi-restraints excluded: chain H residue 449 ARG Chi-restraints excluded: chain H residue 474 LYS Chi-restraints excluded: chain H residue 491 CYS Chi-restraints excluded: chain H residue 505 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.084671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.058230 restraints weight = 36407.127| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.19 r_work: 0.2877 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14757 Z= 0.190 Angle : 0.618 10.994 19992 Z= 0.315 Chirality : 0.045 0.148 2118 Planarity : 0.005 0.055 2616 Dihedral : 4.211 15.153 1968 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.47 % Allowed : 26.14 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.10 (0.19), residues: 1800 helix: 2.62 (0.26), residues: 369 sheet: -0.53 (0.25), residues: 459 loop : -0.62 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 513 TYR 0.015 0.001 TYR I 94 PHE 0.021 0.002 PHE I 68 TRP 0.006 0.001 TRP E 435 HIS 0.003 0.001 HIS G 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (14736) covalent geometry : angle 0.61580 / 0.31 (19950) SS BOND : bond 0.00388 / 0.27 ( 21) SS BOND : angle 1.27394 / 0.83 ( 42) hydrogen bonds : bond 0.03431 / 2.30 ( 574) hydrogen bonds : angle 5.08160 / 3.53 ( 1662) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 269 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 361 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8584 (pp) REVERT: B 381 GLN cc_start: 0.9183 (mt0) cc_final: 0.8960 (mm-40) REVERT: C 76 LYS cc_start: 0.9403 (mtpt) cc_final: 0.9167 (mtpp) REVERT: C 87 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8506 (ptpp) REVERT: F 46 GLU cc_start: 0.8418 (pt0) cc_final: 0.7992 (pm20) REVERT: F 68 PHE cc_start: 0.7975 (m-10) cc_final: 0.7580 (m-10) REVERT: F 73 ASP cc_start: 0.8468 (t0) cc_final: 0.7806 (t0) REVERT: F 83 MET cc_start: 0.8253 (mmm) cc_final: 0.7905 (mmm) REVERT: F 102 LEU cc_start: 0.8853 (mt) cc_final: 0.8608 (mp) REVERT: I 76 LYS cc_start: 0.9352 (mtpt) cc_final: 0.9141 (mtmt) REVERT: I 87 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8633 (ptpp) REVERT: G 52 ASP cc_start: 0.8989 (p0) cc_final: 0.8768 (p0) REVERT: E 360 MET cc_start: 0.8930 (ttp) cc_final: 0.8720 (ptm) REVERT: E 381 GLN cc_start: 0.9242 (mt0) cc_final: 0.9025 (mm-40) REVERT: E 501 ASP cc_start: 0.8976 (t0) cc_final: 0.8694 (t0) REVERT: H 358 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.8992 (m) REVERT: H 361 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8535 (pp) REVERT: H 362 ASP cc_start: 0.8722 (p0) cc_final: 0.7949 (t0) REVERT: H 370 GLN cc_start: 0.8673 (tm-30) cc_final: 0.8324 (tm130) REVERT: H 381 GLN cc_start: 0.9233 (mt0) cc_final: 0.8974 (mm-40) REVERT: H 448 GLU cc_start: 0.8722 (tp30) cc_final: 0.8488 (mm-30) REVERT: H 449 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.8772 (mtp-110) outliers start: 55 outliers final: 28 residues processed: 295 average time/residue: 0.4838 time to fit residues: 158.8607 Evaluate side-chains 296 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 262 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 505 TYR Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 400 GLU Chi-restraints excluded: chain H residue 449 ARG Chi-restraints excluded: chain H residue 474 LYS Chi-restraints excluded: chain H residue 491 CYS Chi-restraints excluded: chain H residue 505 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 118 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 66 optimal weight: 0.0770 chunk 33 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.085188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.058737 restraints weight = 36234.212| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.19 r_work: 0.2881 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14757 Z= 0.166 Angle : 0.624 11.202 19992 Z= 0.316 Chirality : 0.045 0.148 2118 Planarity : 0.005 0.054 2616 Dihedral : 4.220 15.301 1968 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.84 % Allowed : 26.70 % Favored : 70.45 % 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: 0.10 (0.19), residues: 1800 helix: 2.64 (0.26), residues: 369 sheet: -0.55 (0.25), residues: 459 loop : -0.62 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 513 TYR 0.016 0.001 TYR E 367 PHE 0.020 0.002 PHE G 277 TRP 0.006 0.001 TRP E 435 HIS 0.003 0.001 HIS G 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (14736) covalent geometry : angle 0.62254 / 0.31 (19950) SS BOND : bond 0.00379 / 0.26 ( 21) SS BOND : angle 1.18795 / 0.81 ( 42) hydrogen bonds : bond 0.03407 / 2.27 ( 574) hydrogen bonds : angle 5.06894 / 3.52 ( 1662) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 266 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 361 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8606 (pp) REVERT: B 381 GLN cc_start: 0.9189 (mt0) cc_final: 0.8972 (mm-40) REVERT: C 68 PHE cc_start: 0.7809 (m-10) cc_final: 0.7529 (m-10) REVERT: C 76 LYS cc_start: 0.9405 (mtpt) cc_final: 0.9174 (mtpp) REVERT: C 87 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8510 (ptpp) REVERT: F 46 GLU cc_start: 0.8429 (pt0) cc_final: 0.8030 (pm20) REVERT: F 65 LYS cc_start: 0.9612 (mtpm) cc_final: 0.9397 (mtpp) REVERT: F 73 ASP cc_start: 0.8473 (t0) cc_final: 0.7801 (t0) REVERT: F 87 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8422 (ptpp) REVERT: F 102 LEU cc_start: 0.8859 (mt) cc_final: 0.8625 (mp) REVERT: I 87 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8682 (ptpp) REVERT: G 52 ASP cc_start: 0.8985 (p0) cc_final: 0.8768 (p0) REVERT: E 381 GLN cc_start: 0.9236 (mt0) cc_final: 0.9024 (mm-40) REVERT: E 501 ASP cc_start: 0.8999 (t0) cc_final: 0.8713 (t0) REVERT: H 358 THR cc_start: 0.9214 (OUTLIER) cc_final: 0.9003 (m) REVERT: H 361 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8561 (pp) REVERT: H 362 ASP cc_start: 0.8715 (p0) cc_final: 0.7908 (t0) REVERT: H 370 GLN cc_start: 0.8666 (tm-30) cc_final: 0.8277 (tm130) REVERT: H 381 GLN cc_start: 0.9239 (mt0) cc_final: 0.8910 (mm-40) REVERT: H 448 GLU cc_start: 0.8732 (tp30) cc_final: 0.8506 (mm-30) REVERT: H 449 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8785 (mtp-110) outliers start: 45 outliers final: 26 residues processed: 285 average time/residue: 0.4757 time to fit residues: 151.0538 Evaluate side-chains 291 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 258 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 400 GLU Chi-restraints excluded: chain E residue 505 TYR Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 400 GLU Chi-restraints excluded: chain H residue 449 ARG Chi-restraints excluded: chain H residue 474 LYS Chi-restraints excluded: chain H residue 505 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 75 optimal weight: 0.0870 chunk 131 optimal weight: 0.0770 chunk 133 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 chunk 121 optimal weight: 0.0470 chunk 15 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 overall best weight: 0.3014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 414 ASN ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 414 ASN ** E 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.087142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.060987 restraints weight = 36281.158| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.19 r_work: 0.2936 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14757 Z= 0.116 Angle : 0.621 11.696 19992 Z= 0.311 Chirality : 0.044 0.145 2118 Planarity : 0.005 0.054 2616 Dihedral : 4.121 16.162 1968 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.21 % Allowed : 27.90 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.08 (0.19), residues: 1800 helix: 2.59 (0.27), residues: 369 sheet: -0.55 (0.26), residues: 438 loop : -0.62 (0.18), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 57 TYR 0.015 0.001 TYR E 505 PHE 0.018 0.001 PHE A 277 TRP 0.006 0.001 TRP E 435 HIS 0.002 0.000 HIS H 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (14736) covalent geometry : angle 0.61961 / 0.31 (19950) SS BOND : bond 0.00286 / 0.19 ( 21) SS BOND : angle 1.00596 / 0.71 ( 42) hydrogen bonds : bond 0.03346 / 2.23 ( 574) hydrogen bonds : angle 4.95325 / 3.44 ( 1662) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 283 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 SER cc_start: 0.9268 (m) cc_final: 0.8990 (t) REVERT: B 361 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8602 (pp) REVERT: B 381 GLN cc_start: 0.9180 (mt0) cc_final: 0.8962 (mm-40) REVERT: C 67 ARG cc_start: 0.8737 (mtm-85) cc_final: 0.7983 (ptm-80) REVERT: C 83 MET cc_start: 0.8237 (mmt) cc_final: 0.8020 (mmt) REVERT: C 87 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8366 (ptpp) REVERT: F 46 GLU cc_start: 0.8384 (pt0) cc_final: 0.7899 (pm20) REVERT: F 65 LYS cc_start: 0.9586 (mtpm) cc_final: 0.9378 (mtpp) REVERT: F 68 PHE cc_start: 0.7547 (m-10) cc_final: 0.6469 (m-10) REVERT: F 73 ASP cc_start: 0.8482 (t0) cc_final: 0.7801 (t0) REVERT: F 83 MET cc_start: 0.8301 (mmm) cc_final: 0.7990 (mmm) REVERT: F 102 LEU cc_start: 0.8813 (mt) cc_final: 0.8595 (mp) REVERT: I 68 PHE cc_start: 0.7318 (m-10) cc_final: 0.6706 (m-10) REVERT: I 73 ASP cc_start: 0.8658 (t0) cc_final: 0.8055 (t0) REVERT: I 80 TYR cc_start: 0.7827 (m-80) cc_final: 0.7618 (m-80) REVERT: I 87 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8703 (ptpp) REVERT: G 52 ASP cc_start: 0.8918 (p0) cc_final: 0.8685 (p0) REVERT: E 381 GLN cc_start: 0.9220 (mt0) cc_final: 0.9017 (mm-40) REVERT: E 501 ASP cc_start: 0.8990 (t0) cc_final: 0.8739 (t0) REVERT: H 361 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8499 (pp) REVERT: H 362 ASP cc_start: 0.8667 (p0) cc_final: 0.7891 (t0) REVERT: H 370 GLN cc_start: 0.8652 (tm-30) cc_final: 0.8280 (tm130) REVERT: H 381 GLN cc_start: 0.9238 (mt0) cc_final: 0.8929 (mm-40) REVERT: H 448 GLU cc_start: 0.8725 (tp30) cc_final: 0.8524 (mm-30) REVERT: H 449 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8717 (mtp-110) REVERT: H 474 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.8927 (pttm) outliers start: 35 outliers final: 17 residues processed: 298 average time/residue: 0.4332 time to fit residues: 143.8047 Evaluate side-chains 294 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 271 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 505 TYR Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 400 GLU Chi-restraints excluded: chain H residue 449 ARG Chi-restraints excluded: chain H residue 474 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 162 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 174 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.085972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.059586 restraints weight = 36205.356| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.21 r_work: 0.2908 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14757 Z= 0.161 Angle : 0.645 12.316 19992 Z= 0.324 Chirality : 0.045 0.183 2118 Planarity : 0.005 0.055 2616 Dihedral : 4.254 20.808 1968 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.89 % Allowed : 28.79 % Favored : 69.32 % 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: 0.08 (0.19), residues: 1800 helix: 2.50 (0.26), residues: 369 sheet: -0.54 (0.25), residues: 459 loop : -0.58 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 513 TYR 0.014 0.001 TYR H 505 PHE 0.022 0.002 PHE B 481 TRP 0.006 0.001 TRP C 109 HIS 0.003 0.001 HIS D 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (14736) covalent geometry : angle 0.64268 / 0.32 (19950) SS BOND : bond 0.00491 / 0.30 ( 21) SS BOND : angle 1.35683 / 0.89 ( 42) hydrogen bonds : bond 0.03387 / 2.28 ( 574) hydrogen bonds : angle 5.05494 / 3.51 ( 1662) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 275 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 361 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8629 (pp) REVERT: B 381 GLN cc_start: 0.9179 (mt0) cc_final: 0.8961 (mm-40) REVERT: C 65 LYS cc_start: 0.9570 (mtpm) cc_final: 0.9315 (mtpp) REVERT: C 67 ARG cc_start: 0.8873 (mtm-85) cc_final: 0.8261 (ptm-80) REVERT: C 68 PHE cc_start: 0.7340 (m-10) cc_final: 0.7030 (m-10) REVERT: C 87 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8359 (ptpp) REVERT: F 46 GLU cc_start: 0.8408 (pt0) cc_final: 0.7903 (pm20) REVERT: F 65 LYS cc_start: 0.9591 (mtpm) cc_final: 0.9391 (mtpp) REVERT: F 68 PHE cc_start: 0.7494 (m-10) cc_final: 0.6454 (m-10) REVERT: F 73 ASP cc_start: 0.8498 (t0) cc_final: 0.7807 (t0) REVERT: F 87 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8382 (ptpp) REVERT: F 95 TYR cc_start: 0.8785 (m-10) cc_final: 0.8564 (m-10) REVERT: F 100 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.7767 (ptm-80) REVERT: F 102 LEU cc_start: 0.8859 (mt) cc_final: 0.8635 (mp) REVERT: I 73 ASP cc_start: 0.8653 (t0) cc_final: 0.8088 (t0) REVERT: I 87 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8713 (ptpp) REVERT: G 52 ASP cc_start: 0.8952 (p0) cc_final: 0.8717 (p0) REVERT: E 360 MET cc_start: 0.8889 (ttp) cc_final: 0.8548 (ptm) REVERT: E 501 ASP cc_start: 0.8992 (t0) cc_final: 0.8729 (t0) REVERT: H 361 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8516 (pp) REVERT: H 362 ASP cc_start: 0.8667 (p0) cc_final: 0.7913 (t0) REVERT: H 370 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8243 (tm-30) REVERT: H 381 GLN cc_start: 0.9205 (mt0) cc_final: 0.8930 (mm-40) REVERT: H 448 GLU cc_start: 0.8771 (tp30) cc_final: 0.8564 (mm-30) REVERT: H 449 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.8745 (mtp-110) REVERT: H 474 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8971 (pttm) outliers start: 30 outliers final: 17 residues processed: 291 average time/residue: 0.5064 time to fit residues: 163.7972 Evaluate side-chains 294 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 269 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 505 TYR Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 400 GLU Chi-restraints excluded: chain H residue 449 ARG Chi-restraints excluded: chain H residue 474 LYS Chi-restraints excluded: chain H residue 491 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 116 optimal weight: 3.9990 chunk 176 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 175 optimal weight: 6.9990 chunk 152 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.086195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.059765 restraints weight = 36465.117| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.16 r_work: 0.2887 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14757 Z= 0.194 Angle : 0.649 11.510 19992 Z= 0.329 Chirality : 0.046 0.173 2118 Planarity : 0.005 0.055 2616 Dihedral : 4.416 25.222 1968 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.89 % Allowed : 28.22 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.06 (0.19), residues: 1800 helix: 2.53 (0.27), residues: 363 sheet: -0.60 (0.25), residues: 459 loop : -0.56 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 57 TYR 0.015 0.002 TYR I 94 PHE 0.029 0.002 PHE I 68 TRP 0.006 0.001 TRP G 77 HIS 0.003 0.001 HIS G 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (14736) covalent geometry : angle 0.64684 / 0.33 (19950) SS BOND : bond 0.00407 / 0.28 ( 21) SS BOND : angle 1.33993 / 0.88 ( 42) hydrogen bonds : bond 0.03450 / 2.31 ( 574) hydrogen bonds : angle 5.15744 / 3.58 ( 1662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4715.13 seconds wall clock time: 81 minutes 20.15 seconds (4880.15 seconds total)