Starting phenix.real_space_refine on Fri Jun 5 16:36:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ef8_9046/06_2026/6ef8_9046_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ef8_9046/06_2026/6ef8_9046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ef8_9046/06_2026/6ef8_9046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ef8_9046/06_2026/6ef8_9046.map" model { file = "/net/cci-nas-00/data/ceres_data/6ef8_9046/06_2026/6ef8_9046_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ef8_9046/06_2026/6ef8_9046_neut.cif" } resolution = 3.7 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 ------------------------------------------------------------------------------- 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= 0.101 sd= 0.576 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: 5 Type Number sf(0) Gaussians Fe 42 7.16 5 S 140 5.16 5 C 14385 2.51 5 N 3927 2.21 5 O 4417 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22911 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3015 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 388} Chain: "A" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 258 Unusual residues: {'HEC': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 4.02, per 1000 atoms: 0.18 Number of scatterers: 22911 At special positions: 0 Unit cell: (85.05, 84, 358.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 42 26.01 S 140 16.00 O 4417 8.00 N 3927 7.00 C 14385 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=119, symmetry=0 Number of additional bonds: simple=119, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.0 seconds 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5068 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 28 sheets defined 17.0% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 8 through 13 removed outlier: 4.202A pdb=" N CYS A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N HIS A 13 " --> pdb=" O CYS A 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 8 through 13' Processing helix chain 'A' and resid 34 through 38 removed outlier: 3.509A pdb=" N LEU A 37 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 91 removed outlier: 3.527A pdb=" N LYS A 91 " --> pdb=" O TRP A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.898A pdb=" N CYS A 143 " --> pdb=" O CYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 241 Processing helix chain 'A' and resid 266 through 276 Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 313 through 317 removed outlier: 4.339A pdb=" N ALA A 316 " --> pdb=" O ASP A 313 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU A 317 " --> pdb=" O ASP A 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 317' Processing helix chain 'A' and resid 376 through 384 Processing helix chain 'A' and resid 398 through 402 Processing helix chain 'B' and resid 8 through 13 removed outlier: 4.201A pdb=" N CYS B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS B 13 " --> pdb=" O CYS B 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 8 through 13' Processing helix chain 'B' and resid 34 through 38 removed outlier: 3.509A pdb=" N LEU B 37 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 91 removed outlier: 3.526A pdb=" N LYS B 91 " --> pdb=" O TRP B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 removed outlier: 3.898A pdb=" N CYS B 143 " --> pdb=" O CYS B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 241 Processing helix chain 'B' and resid 266 through 276 Processing helix chain 'B' and resid 302 through 309 Processing helix chain 'B' and resid 313 through 317 removed outlier: 4.340A pdb=" N ALA B 316 " --> pdb=" O ASP B 313 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU B 317 " --> pdb=" O ASP B 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 313 through 317' Processing helix chain 'B' and resid 376 through 384 Processing helix chain 'B' and resid 398 through 402 Processing helix chain 'C' and resid 8 through 13 removed outlier: 4.201A pdb=" N CYS C 12 " --> pdb=" O GLU C 8 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N HIS C 13 " --> pdb=" O CYS C 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 8 through 13' Processing helix chain 'C' and resid 34 through 38 removed outlier: 3.508A pdb=" N LEU C 37 " --> pdb=" O GLY C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 91 removed outlier: 3.526A pdb=" N LYS C 91 " --> pdb=" O TRP C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 143 removed outlier: 3.897A pdb=" N CYS C 143 " --> pdb=" O CYS C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 266 through 276 Processing helix chain 'C' and resid 302 through 309 Processing helix chain 'C' and resid 313 through 317 removed outlier: 4.339A pdb=" N ALA C 316 " --> pdb=" O ASP C 313 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU C 317 " --> pdb=" O ASP C 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 313 through 317' Processing helix chain 'C' and resid 376 through 384 Processing helix chain 'C' and resid 398 through 402 Processing helix chain 'D' and resid 8 through 13 removed outlier: 4.201A pdb=" N CYS D 12 " --> pdb=" O GLU D 8 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N HIS D 13 " --> pdb=" O CYS D 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 8 through 13' Processing helix chain 'D' and resid 34 through 38 removed outlier: 3.509A pdb=" N LEU D 37 " --> pdb=" O GLY D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 91 removed outlier: 3.526A pdb=" N LYS D 91 " --> pdb=" O TRP D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 143 removed outlier: 3.898A pdb=" N CYS D 143 " --> pdb=" O CYS D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 241 Processing helix chain 'D' and resid 266 through 276 Processing helix chain 'D' and resid 302 through 309 Processing helix chain 'D' and resid 313 through 317 removed outlier: 4.339A pdb=" N ALA D 316 " --> pdb=" O ASP D 313 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU D 317 " --> pdb=" O ASP D 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 313 through 317' Processing helix chain 'D' and resid 376 through 384 Processing helix chain 'D' and resid 398 through 402 Processing helix chain 'E' and resid 8 through 13 removed outlier: 4.201A pdb=" N CYS E 12 " --> pdb=" O GLU E 8 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N HIS E 13 " --> pdb=" O CYS E 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 8 through 13' Processing helix chain 'E' and resid 34 through 38 removed outlier: 3.509A pdb=" N LEU E 37 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 91 removed outlier: 3.526A pdb=" N LYS E 91 " --> pdb=" O TRP E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 143 removed outlier: 3.898A pdb=" N CYS E 143 " --> pdb=" O CYS E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 241 Processing helix chain 'E' and resid 266 through 276 Processing helix chain 'E' and resid 302 through 309 Processing helix chain 'E' and resid 313 through 317 removed outlier: 4.339A pdb=" N ALA E 316 " --> pdb=" O ASP E 313 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU E 317 " --> pdb=" O ASP E 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 313 through 317' Processing helix chain 'E' and resid 376 through 384 Processing helix chain 'E' and resid 398 through 402 Processing helix chain 'F' and resid 8 through 13 removed outlier: 4.201A pdb=" N CYS F 12 " --> pdb=" O GLU F 8 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N HIS F 13 " --> pdb=" O CYS F 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 8 through 13' Processing helix chain 'F' and resid 34 through 38 removed outlier: 3.509A pdb=" N LEU F 37 " --> pdb=" O GLY F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 91 removed outlier: 3.527A pdb=" N LYS F 91 " --> pdb=" O TRP F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 143 removed outlier: 3.898A pdb=" N CYS F 143 " --> pdb=" O CYS F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 241 Processing helix chain 'F' and resid 266 through 276 Processing helix chain 'F' and resid 302 through 309 Processing helix chain 'F' and resid 313 through 317 removed outlier: 4.339A pdb=" N ALA F 316 " --> pdb=" O ASP F 313 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU F 317 " --> pdb=" O ASP F 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 313 through 317' Processing helix chain 'F' and resid 376 through 384 Processing helix chain 'F' and resid 398 through 402 Processing helix chain 'G' and resid 8 through 13 removed outlier: 4.201A pdb=" N CYS G 12 " --> pdb=" O GLU G 8 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N HIS G 13 " --> pdb=" O CYS G 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 8 through 13' Processing helix chain 'G' and resid 34 through 38 removed outlier: 3.509A pdb=" N LEU G 37 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 91 removed outlier: 3.527A pdb=" N LYS G 91 " --> pdb=" O TRP G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 143 removed outlier: 3.898A pdb=" N CYS G 143 " --> pdb=" O CYS G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 241 Processing helix chain 'G' and resid 266 through 276 Processing helix chain 'G' and resid 302 through 309 Processing helix chain 'G' and resid 313 through 317 removed outlier: 4.339A pdb=" N ALA G 316 " --> pdb=" O ASP G 313 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU G 317 " --> pdb=" O ASP G 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 313 through 317' Processing helix chain 'G' and resid 376 through 384 Processing helix chain 'G' and resid 398 through 402 Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 95 removed outlier: 3.578A pdb=" N TRP A 95 " --> pdb=" O ASN A 101 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 151 through 152 Processing sheet with id=AA3, first strand: chain 'A' and resid 260 through 264 removed outlier: 4.078A pdb=" N VAL A 326 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 354 through 356 removed outlier: 3.930A pdb=" N ASN A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 93 through 95 removed outlier: 3.577A pdb=" N TRP B 95 " --> pdb=" O ASN B 101 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 151 through 152 Processing sheet with id=AA7, first strand: chain 'B' and resid 260 through 264 removed outlier: 4.078A pdb=" N VAL B 326 " --> pdb=" O GLY B 260 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 354 through 356 removed outlier: 3.931A pdb=" N ASN B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 93 through 95 removed outlier: 3.577A pdb=" N TRP C 95 " --> pdb=" O ASN C 101 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 151 through 152 Processing sheet with id=AB2, first strand: chain 'C' and resid 260 through 264 removed outlier: 4.078A pdb=" N VAL C 326 " --> pdb=" O GLY C 260 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 354 through 356 removed outlier: 3.931A pdb=" N ASN C 360 " --> pdb=" O ASP C 356 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 93 through 95 removed outlier: 3.578A pdb=" N TRP D 95 " --> pdb=" O ASN D 101 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 151 through 152 Processing sheet with id=AB6, first strand: chain 'D' and resid 260 through 264 removed outlier: 4.078A pdb=" N VAL D 326 " --> pdb=" O GLY D 260 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 354 through 356 removed outlier: 3.931A pdb=" N ASN D 360 " --> pdb=" O ASP D 356 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 93 through 95 removed outlier: 3.577A pdb=" N TRP E 95 " --> pdb=" O ASN E 101 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 151 through 152 Processing sheet with id=AC1, first strand: chain 'E' and resid 260 through 264 removed outlier: 4.078A pdb=" N VAL E 326 " --> pdb=" O GLY E 260 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 354 through 356 removed outlier: 3.932A pdb=" N ASN E 360 " --> pdb=" O ASP E 356 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 93 through 95 removed outlier: 3.578A pdb=" N TRP F 95 " --> pdb=" O ASN F 101 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 151 through 152 Processing sheet with id=AC5, first strand: chain 'F' and resid 260 through 264 removed outlier: 4.078A pdb=" N VAL F 326 " --> pdb=" O GLY F 260 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 354 through 356 removed outlier: 3.931A pdb=" N ASN F 360 " --> pdb=" O ASP F 356 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 93 through 95 removed outlier: 3.577A pdb=" N TRP G 95 " --> pdb=" O ASN G 101 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 151 through 152 Processing sheet with id=AC9, first strand: chain 'G' and resid 260 through 264 removed outlier: 4.079A pdb=" N VAL G 326 " --> pdb=" O GLY G 260 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 354 through 356 removed outlier: 3.931A pdb=" N ASN G 360 " --> pdb=" O ASP G 356 " (cutoff:3.500A) 252 hydrogen bonds defined for protein. 504 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.53 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 10137 1.39 - 1.56: 13226 1.56 - 1.73: 3 1.73 - 1.90: 196 1.90 - 2.06: 168 Bond restraints: 23730 Sorted by residual: bond pdb=" CB CYS G 140 " pdb=" SG CYS G 140 " ideal model delta sigma weight residual 1.808 1.753 0.055 3.30e-02 9.18e+02 2.82e+00 bond pdb=" CB CYS E 140 " pdb=" SG CYS E 140 " ideal model delta sigma weight residual 1.808 1.753 0.055 3.30e-02 9.18e+02 2.81e+00 bond pdb=" CB CYS D 140 " pdb=" SG CYS D 140 " ideal model delta sigma weight residual 1.808 1.753 0.055 3.30e-02 9.18e+02 2.81e+00 bond pdb=" CB CYS C 140 " pdb=" SG CYS C 140 " ideal model delta sigma weight residual 1.808 1.753 0.055 3.30e-02 9.18e+02 2.80e+00 bond pdb=" CB CYS A 140 " pdb=" SG CYS A 140 " ideal model delta sigma weight residual 1.808 1.753 0.055 3.30e-02 9.18e+02 2.75e+00 ... (remaining 23725 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 31086 2.49 - 4.97: 1327 4.97 - 7.46: 242 7.46 - 9.94: 175 9.94 - 12.43: 63 Bond angle restraints: 32893 Sorted by residual: angle pdb=" N ILE A 188 " pdb=" CA ILE A 188 " pdb=" C ILE A 188 " ideal model delta sigma weight residual 109.34 120.83 -11.49 2.08e+00 2.31e-01 3.05e+01 angle pdb=" N ILE D 188 " pdb=" CA ILE D 188 " pdb=" C ILE D 188 " ideal model delta sigma weight residual 109.34 120.83 -11.49 2.08e+00 2.31e-01 3.05e+01 angle pdb=" N ILE E 188 " pdb=" CA ILE E 188 " pdb=" C ILE E 188 " ideal model delta sigma weight residual 109.34 120.82 -11.48 2.08e+00 2.31e-01 3.05e+01 angle pdb=" N ILE G 188 " pdb=" CA ILE G 188 " pdb=" C ILE G 188 " ideal model delta sigma weight residual 109.34 120.82 -11.48 2.08e+00 2.31e-01 3.05e+01 angle pdb=" N ILE C 188 " pdb=" CA ILE C 188 " pdb=" C ILE C 188 " ideal model delta sigma weight residual 109.34 120.82 -11.48 2.08e+00 2.31e-01 3.04e+01 ... (remaining 32888 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 12120 17.44 - 34.88: 529 34.88 - 52.32: 84 52.32 - 69.76: 42 69.76 - 87.20: 98 Dihedral angle restraints: 12873 sinusoidal: 4809 harmonic: 8064 Sorted by residual: dihedral pdb=" CA ASN E 327 " pdb=" C ASN E 327 " pdb=" N CYS E 328 " pdb=" CA CYS E 328 " ideal model delta harmonic sigma weight residual 180.00 132.00 48.00 0 5.00e+00 4.00e-02 9.22e+01 dihedral pdb=" CA ASN D 327 " pdb=" C ASN D 327 " pdb=" N CYS D 328 " pdb=" CA CYS D 328 " ideal model delta harmonic sigma weight residual 180.00 132.01 47.99 0 5.00e+00 4.00e-02 9.21e+01 dihedral pdb=" CA ASN C 327 " pdb=" C ASN C 327 " pdb=" N CYS C 328 " pdb=" CA CYS C 328 " ideal model delta harmonic sigma weight residual 180.00 132.02 47.98 0 5.00e+00 4.00e-02 9.21e+01 ... (remaining 12870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1917 0.046 - 0.092: 890 0.092 - 0.138: 266 0.138 - 0.184: 63 0.184 - 0.229: 21 Chirality restraints: 3157 Sorted by residual: chirality pdb=" CB VAL E 6 " pdb=" CA VAL E 6 " pdb=" CG1 VAL E 6 " pdb=" CG2 VAL E 6 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB VAL C 6 " pdb=" CA VAL C 6 " pdb=" CG1 VAL C 6 " pdb=" CG2 VAL C 6 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB VAL F 6 " pdb=" CA VAL F 6 " pdb=" CG1 VAL F 6 " pdb=" CG2 VAL F 6 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 3154 not shown) Planarity restraints: 4179 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC C 504 " -0.011 2.00e-02 2.50e+03 5.68e-02 7.25e+01 pdb=" C2C HEC C 504 " 0.153 2.00e-02 2.50e+03 pdb=" C3C HEC C 504 " -0.037 2.00e-02 2.50e+03 pdb=" C4C HEC C 504 " -0.007 2.00e-02 2.50e+03 pdb=" CAC HEC C 504 " -0.013 2.00e-02 2.50e+03 pdb=" CHC HEC C 504 " -0.020 2.00e-02 2.50e+03 pdb=" CHD HEC C 504 " -0.001 2.00e-02 2.50e+03 pdb=" CMC HEC C 504 " -0.057 2.00e-02 2.50e+03 pdb=" NC HEC C 504 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC D 504 " 0.011 2.00e-02 2.50e+03 5.68e-02 7.25e+01 pdb=" C2C HEC D 504 " -0.153 2.00e-02 2.50e+03 pdb=" C3C HEC D 504 " 0.037 2.00e-02 2.50e+03 pdb=" C4C HEC D 504 " 0.006 2.00e-02 2.50e+03 pdb=" CAC HEC D 504 " 0.013 2.00e-02 2.50e+03 pdb=" CHC HEC D 504 " 0.020 2.00e-02 2.50e+03 pdb=" CHD HEC D 504 " 0.001 2.00e-02 2.50e+03 pdb=" CMC HEC D 504 " 0.057 2.00e-02 2.50e+03 pdb=" NC HEC D 504 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC A 504 " -0.011 2.00e-02 2.50e+03 5.68e-02 7.25e+01 pdb=" C2C HEC A 504 " 0.153 2.00e-02 2.50e+03 pdb=" C3C HEC A 504 " -0.037 2.00e-02 2.50e+03 pdb=" C4C HEC A 504 " -0.006 2.00e-02 2.50e+03 pdb=" CAC HEC A 504 " -0.013 2.00e-02 2.50e+03 pdb=" CHC HEC A 504 " -0.020 2.00e-02 2.50e+03 pdb=" CHD HEC A 504 " -0.001 2.00e-02 2.50e+03 pdb=" CMC HEC A 504 " -0.057 2.00e-02 2.50e+03 pdb=" NC HEC A 504 " -0.007 2.00e-02 2.50e+03 ... (remaining 4176 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 332 2.60 - 3.17: 19531 3.17 - 3.75: 37987 3.75 - 4.32: 56439 4.32 - 4.90: 89022 Nonbonded interactions: 203311 Sorted by model distance: nonbonded pdb=" NE2 HIS A 332 " pdb="FE HEC A 501 " model vdw 2.023 3.080 nonbonded pdb=" NE2 HIS D 335 " pdb="FE HEC D 504 " model vdw 2.044 3.080 nonbonded pdb=" NE2 HIS E 335 " pdb="FE HEC E 504 " model vdw 2.044 3.080 nonbonded pdb=" NE2 HIS G 335 " pdb="FE HEC G 504 " model vdw 2.044 3.080 nonbonded pdb=" NE2 HIS C 335 " pdb="FE HEC C 504 " model vdw 2.044 3.080 ... (remaining 203306 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.250 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: 0.320 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 20.140 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 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 : 0.014 0.297 23849 Z= 1.206 Angle : 1.377 12.428 32893 Z= 0.631 Chirality : 0.059 0.229 3157 Planarity : 0.009 0.071 4179 Dihedral : 14.341 87.197 7805 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.49 % Allowed : 11.36 % Favored : 88.15 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.03 (0.12), residues: 2835 helix: -3.87 (0.14), residues: 294 sheet: None (None), residues: 0 loop : -2.84 (0.10), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 333 TYR 0.018 0.002 TYR B 150 PHE 0.021 0.003 PHE B 345 TRP 0.038 0.004 TRP D 238 HIS 0.009 0.003 HIS D 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00693 / 0.29 (23730) covalent geometry : angle 1.37704 / 0.63 (32893) hydrogen bonds : bond 0.24731 / 17.17 ( 252) hydrogen bonds : angle 8.22699 / 5.65 ( 504) Misc. bond : bond 0.18045 / 13.10 ( 119) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 397 time to evaluate : 0.913 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: A 340 ASP cc_start: 0.7961 (m-30) cc_final: 0.7589 (t0) REVERT: C 107 ARG cc_start: 0.8402 (mmp80) cc_final: 0.7649 (mmp80) REVERT: C 111 ASN cc_start: 0.8048 (m-40) cc_final: 0.7843 (m-40) REVERT: D 221 THR cc_start: 0.8498 (t) cc_final: 0.8192 (p) REVERT: D 377 VAL cc_start: 0.9263 (m) cc_final: 0.9060 (t) REVERT: E 235 MET cc_start: 0.8587 (tpt) cc_final: 0.8223 (tpt) REVERT: E 274 ASN cc_start: 0.8392 (m-40) cc_final: 0.8187 (m-40) REVERT: F 10 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8039 (mm-30) REVERT: F 107 ARG cc_start: 0.8468 (mmp80) cc_final: 0.7964 (mmp80) REVERT: F 235 MET cc_start: 0.8427 (tpt) cc_final: 0.8079 (tpt) REVERT: G 10 GLU cc_start: 0.8281 (mm-30) cc_final: 0.8030 (mm-30) REVERT: G 111 ASN cc_start: 0.8372 (m-40) cc_final: 0.8085 (m-40) REVERT: G 377 VAL cc_start: 0.9260 (m) cc_final: 0.9043 (t) outliers start: 0 outliers final: 0 residues processed: 397 average time/residue: 0.1663 time to fit residues: 104.7162 Evaluate side-chains 182 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 20.0000 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 63 HIS A 101 ASN A 111 ASN A 139 HIS A 325 ASN ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 GLN ** A 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 HIS B 101 ASN B 111 ASN B 139 HIS ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 HIS C 101 ASN C 111 ASN C 139 HIS ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 373 GLN ** C 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 HIS D 63 HIS D 101 ASN D 111 ASN D 139 HIS ** D 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 GLN ** D 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 HIS E 63 HIS E 101 ASN E 110 HIS E 111 ASN E 139 HIS ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 HIS F 63 HIS F 101 ASN F 111 ASN F 139 HIS ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 373 GLN ** F 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 HIS G 63 HIS G 101 ASN G 111 ASN G 139 HIS ** G 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.080096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.073554 restraints weight = 51106.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.075785 restraints weight = 20852.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.077125 restraints weight = 10703.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.077951 restraints weight = 6353.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.078491 restraints weight = 4171.967| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.324 23849 Z= 0.180 Angle : 0.838 14.858 32893 Z= 0.372 Chirality : 0.045 0.152 3157 Planarity : 0.005 0.074 4179 Dihedral : 15.554 89.897 3430 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.50 % Favored : 88.25 % Rotamer: Outliers : 2.06 % Allowed : 9.62 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.55 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.05 (0.14), residues: 2835 helix: -1.85 (0.24), residues: 336 sheet: None (None), residues: 0 loop : -2.30 (0.12), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 220 TYR 0.018 0.001 TYR B 150 PHE 0.017 0.002 PHE A 351 TRP 0.022 0.002 TRP A 238 HIS 0.011 0.001 HIS F 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.17 (23730) covalent geometry : angle 0.83813 / 0.37 (32893) hydrogen bonds : bond 0.03261 / 2.25 ( 252) hydrogen bonds : angle 4.76081 / 3.20 ( 504) Misc. bond : bond 0.11114 / 7.82 ( 119) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 209 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8629 (mt) cc_final: 0.8221 (mt) REVERT: A 311 LYS cc_start: 0.8321 (mttp) cc_final: 0.8011 (mtpp) REVERT: A 340 ASP cc_start: 0.8009 (m-30) cc_final: 0.7701 (t0) REVERT: A 377 VAL cc_start: 0.9267 (m) cc_final: 0.9056 (t) REVERT: B 118 ASN cc_start: 0.8353 (m-40) cc_final: 0.7912 (p0) REVERT: D 36 MET cc_start: 0.8947 (mmt) cc_final: 0.8618 (mmm) REVERT: D 118 ASN cc_start: 0.8306 (m-40) cc_final: 0.8101 (p0) REVERT: D 189 LEU cc_start: 0.8652 (mt) cc_final: 0.8441 (mt) REVERT: D 221 THR cc_start: 0.8529 (t) cc_final: 0.8034 (p) REVERT: D 377 VAL cc_start: 0.9348 (m) cc_final: 0.9126 (t) REVERT: E 377 VAL cc_start: 0.9308 (m) cc_final: 0.9056 (t) REVERT: G 111 ASN cc_start: 0.8375 (m110) cc_final: 0.7990 (m-40) REVERT: G 118 ASN cc_start: 0.8392 (m-40) cc_final: 0.8096 (p0) REVERT: G 252 PRO cc_start: 0.7746 (Cg_exo) cc_final: 0.7528 (Cg_endo) outliers start: 45 outliers final: 20 residues processed: 239 average time/residue: 0.1368 time to fit residues: 55.9404 Evaluate side-chains 175 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 247 HIS Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 351 PHE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 351 PHE Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 351 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 101 optimal weight: 2.9990 chunk 153 optimal weight: 20.0000 chunk 204 optimal weight: 20.0000 chunk 246 optimal weight: 20.0000 chunk 159 optimal weight: 20.0000 chunk 277 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 chunk 175 optimal weight: 0.0970 chunk 20 optimal weight: 9.9990 chunk 209 optimal weight: 10.0000 overall best weight: 5.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 HIS B 52 GLN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN D 404 HIS E 52 GLN E 274 ASN ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 HIS F 52 GLN ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS G 52 GLN ** G 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.076571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.070123 restraints weight = 51225.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.072300 restraints weight = 21270.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.073632 restraints weight = 11004.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.074453 restraints weight = 6526.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.074961 restraints weight = 4296.011| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.333 23849 Z= 0.215 Angle : 0.897 18.503 32893 Z= 0.371 Chirality : 0.046 0.214 3157 Planarity : 0.005 0.056 4179 Dihedral : 15.389 89.292 3430 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.52 % Favored : 87.23 % Rotamer: Outliers : 3.30 % Allowed : 10.16 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.15), residues: 2835 helix: -0.81 (0.29), residues: 336 sheet: None (None), residues: 0 loop : -2.05 (0.12), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 256 TYR 0.018 0.002 TYR B 150 PHE 0.017 0.002 PHE E 31 TRP 0.025 0.002 TRP F 238 HIS 0.011 0.002 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.21 (23730) covalent geometry : angle 0.89659 / 0.37 (32893) hydrogen bonds : bond 0.03048 / 2.10 ( 252) hydrogen bonds : angle 4.61262 / 3.07 ( 504) Misc. bond : bond 0.12114 / 8.38 ( 119) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 187 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8381 (mttp) cc_final: 0.8052 (mtpp) REVERT: A 340 ASP cc_start: 0.7970 (m-30) cc_final: 0.7744 (t0) REVERT: B 68 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7768 (mm-30) REVERT: B 85 ASP cc_start: 0.7812 (m-30) cc_final: 0.7419 (m-30) REVERT: B 118 ASN cc_start: 0.8314 (m-40) cc_final: 0.7943 (p0) REVERT: C 71 MET cc_start: 0.7182 (OUTLIER) cc_final: 0.6786 (ptp) REVERT: C 85 ASP cc_start: 0.8033 (m-30) cc_final: 0.7726 (m-30) REVERT: C 165 ILE cc_start: 0.8754 (mt) cc_final: 0.8544 (mt) REVERT: C 354 ILE cc_start: 0.9174 (mm) cc_final: 0.8964 (mt) REVERT: C 380 MET cc_start: 0.8781 (tpp) cc_final: 0.8527 (tpp) REVERT: D 36 MET cc_start: 0.8899 (mmt) cc_final: 0.8624 (mmm) REVERT: D 221 THR cc_start: 0.8678 (t) cc_final: 0.8261 (p) REVERT: D 340 ASP cc_start: 0.8395 (t0) cc_final: 0.8071 (t0) REVERT: E 107 ARG cc_start: 0.8482 (mmp80) cc_final: 0.8242 (mmp80) REVERT: E 274 ASN cc_start: 0.8277 (m-40) cc_final: 0.7978 (m-40) REVERT: F 274 ASN cc_start: 0.8528 (m-40) cc_final: 0.8323 (m-40) REVERT: G 189 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8059 (mt) outliers start: 72 outliers final: 39 residues processed: 232 average time/residue: 0.1313 time to fit residues: 53.1988 Evaluate side-chains 200 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 159 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain D residue 247 HIS Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 351 PHE Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 351 PHE Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 325 ASN Chi-restraints excluded: chain G residue 351 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 110 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 71 optimal weight: 30.0000 chunk 211 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 175 optimal weight: 0.0040 chunk 119 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 overall best weight: 5.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 ASN ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 HIS C 404 HIS ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 404 HIS ** 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 = 0.2962 r_free = 0.2962 target = 0.076613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.070221 restraints weight = 51549.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.072397 restraints weight = 21319.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.073715 restraints weight = 11004.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.074528 restraints weight = 6538.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.075035 restraints weight = 4274.623| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.275 23849 Z= 0.198 Angle : 0.856 17.896 32893 Z= 0.355 Chirality : 0.045 0.173 3157 Planarity : 0.005 0.047 4179 Dihedral : 15.262 89.989 3430 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.53 % Favored : 88.22 % Rotamer: Outliers : 3.89 % Allowed : 11.36 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.16), residues: 2835 helix: -0.48 (0.30), residues: 336 sheet: None (None), residues: 0 loop : -1.89 (0.13), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 333 TYR 0.016 0.001 TYR B 150 PHE 0.017 0.002 PHE F 86 TRP 0.023 0.002 TRP D 238 HIS 0.008 0.002 HIS G 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.19 (23730) covalent geometry : angle 0.85587 / 0.35 (32893) hydrogen bonds : bond 0.02819 / 1.95 ( 252) hydrogen bonds : angle 4.54121 / 2.99 ( 504) Misc. bond : bond 0.11377 / 7.79 ( 119) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 172 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 160 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8460 (t) REVERT: B 85 ASP cc_start: 0.7932 (m-30) cc_final: 0.7457 (m-30) REVERT: B 118 ASN cc_start: 0.8185 (m-40) cc_final: 0.7893 (p0) REVERT: B 354 ILE cc_start: 0.9143 (mm) cc_final: 0.8839 (mt) REVERT: C 380 MET cc_start: 0.8794 (tpp) cc_final: 0.8536 (tpp) REVERT: D 36 MET cc_start: 0.8883 (mmt) cc_final: 0.8617 (mmm) REVERT: D 221 THR cc_start: 0.8583 (t) cc_final: 0.8120 (p) REVERT: D 340 ASP cc_start: 0.8466 (t0) cc_final: 0.8118 (t0) REVERT: E 342 MET cc_start: 0.7688 (ttm) cc_final: 0.7423 (ttm) REVERT: F 107 ARG cc_start: 0.8523 (mmp80) cc_final: 0.8220 (mmp80) REVERT: F 340 ASP cc_start: 0.8532 (t0) cc_final: 0.8223 (t0) REVERT: G 189 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8149 (mt) outliers start: 85 outliers final: 53 residues processed: 228 average time/residue: 0.1384 time to fit residues: 54.5894 Evaluate side-chains 213 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 158 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 CYS Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain B residue 9 CYS Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 351 PHE Chi-restraints excluded: chain D residue 9 CYS Chi-restraints excluded: chain D residue 247 HIS Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 351 PHE Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 9 CYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 351 PHE Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 325 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 255 optimal weight: 20.0000 chunk 178 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 230 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 270 optimal weight: 20.0000 chunk 205 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 151 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 63 optimal weight: 20.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN A 274 ASN A 286 GLN A 325 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 HIS E 286 GLN F 51 HIS ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 404 HIS ** 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 = 0.2904 r_free = 0.2904 target = 0.073545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.067121 restraints weight = 51634.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.069276 restraints weight = 21466.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.070579 restraints weight = 11127.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.071392 restraints weight = 6670.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.071906 restraints weight = 4413.658| |-----------------------------------------------------------------------------| r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.416 23849 Z= 0.279 Angle : 0.957 20.329 32893 Z= 0.393 Chirality : 0.047 0.178 3157 Planarity : 0.005 0.049 4179 Dihedral : 15.608 89.903 3430 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.25 % Allowed : 14.07 % Favored : 85.68 % Rotamer: Outliers : 4.49 % Allowed : 11.36 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.16), residues: 2835 helix: -0.66 (0.29), residues: 336 sheet: None (None), residues: 0 loop : -1.90 (0.13), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 333 TYR 0.018 0.002 TYR B 150 PHE 0.027 0.003 PHE B 86 TRP 0.022 0.003 TRP D 238 HIS 0.010 0.002 HIS A 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00728 / 0.27 (23730) covalent geometry : angle 0.95711 / 0.39 (32893) hydrogen bonds : bond 0.03044 / 2.11 ( 252) hydrogen bonds : angle 4.84983 / 3.18 ( 504) Misc. bond : bond 0.15163 / 10.55 ( 119) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 162 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: A 107 ARG cc_start: 0.8478 (mmp80) cc_final: 0.8232 (mmp80) REVERT: A 160 THR cc_start: 0.8700 (OUTLIER) cc_final: 0.8483 (t) REVERT: B 85 ASP cc_start: 0.8060 (m-30) cc_final: 0.7750 (m-30) REVERT: B 118 ASN cc_start: 0.8259 (m-40) cc_final: 0.7934 (p0) REVERT: B 247 HIS cc_start: 0.8947 (OUTLIER) cc_final: 0.8074 (p-80) REVERT: B 354 ILE cc_start: 0.9103 (mm) cc_final: 0.8782 (mt) REVERT: C 85 ASP cc_start: 0.8152 (m-30) cc_final: 0.7696 (m-30) REVERT: D 36 MET cc_start: 0.8916 (mmt) cc_final: 0.8671 (mmm) REVERT: D 221 THR cc_start: 0.8637 (t) cc_final: 0.8276 (p) REVERT: D 274 ASN cc_start: 0.8168 (m-40) cc_final: 0.7791 (m-40) REVERT: D 340 ASP cc_start: 0.8547 (t0) cc_final: 0.8179 (t0) REVERT: E 138 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7314 (tp) REVERT: F 107 ARG cc_start: 0.8549 (mmp80) cc_final: 0.8347 (mmp80) REVERT: F 118 ASN cc_start: 0.8222 (m-40) cc_final: 0.7820 (p0) REVERT: F 235 MET cc_start: 0.7732 (tpt) cc_final: 0.7302 (tpt) REVERT: F 342 MET cc_start: 0.8910 (tpp) cc_final: 0.8417 (tpp) REVERT: G 189 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8391 (mt) outliers start: 98 outliers final: 69 residues processed: 236 average time/residue: 0.1307 time to fit residues: 53.9076 Evaluate side-chains 221 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 148 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 CYS Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain B residue 9 CYS Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 247 HIS Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain C residue 9 CYS Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 351 PHE Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 247 HIS Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 351 PHE Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 9 CYS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 351 PHE Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 325 ASN Chi-restraints excluded: chain G residue 331 CYS Chi-restraints excluded: chain G residue 351 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 151 optimal weight: 30.0000 chunk 139 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 275 optimal weight: 8.9990 chunk 251 optimal weight: 5.9990 chunk 175 optimal weight: 8.9990 chunk 42 optimal weight: 0.1980 chunk 140 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 94 optimal weight: 0.0270 overall best weight: 3.6444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN A 325 ASN ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 HIS ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.077392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.070998 restraints weight = 51272.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.073193 restraints weight = 21221.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.074502 restraints weight = 10900.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.075333 restraints weight = 6483.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.075857 restraints weight = 4203.308| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.244 23849 Z= 0.159 Angle : 0.800 16.077 32893 Z= 0.337 Chirality : 0.044 0.170 3157 Planarity : 0.004 0.046 4179 Dihedral : 15.174 89.983 3430 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.22 % Favored : 88.54 % Rotamer: Outliers : 3.57 % Allowed : 13.23 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.16), residues: 2835 helix: -0.37 (0.30), residues: 336 sheet: None (None), residues: 0 loop : -1.79 (0.13), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 333 TYR 0.015 0.001 TYR F 150 PHE 0.013 0.002 PHE F 86 TRP 0.023 0.002 TRP D 238 HIS 0.007 0.001 HIS E 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.15 (23730) covalent geometry : angle 0.80008 / 0.34 (32893) hydrogen bonds : bond 0.02656 / 1.85 ( 252) hydrogen bonds : angle 4.52189 / 2.96 ( 504) Misc. bond : bond 0.09086 / 6.05 ( 119) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 178 time to evaluate : 0.851 Fit side-chains REVERT: A 311 LYS cc_start: 0.8569 (mttp) cc_final: 0.8234 (mtpp) REVERT: A 342 MET cc_start: 0.8917 (tpp) cc_final: 0.8299 (ttm) REVERT: B 85 ASP cc_start: 0.7867 (m-30) cc_final: 0.7434 (m-30) REVERT: B 247 HIS cc_start: 0.8789 (OUTLIER) cc_final: 0.8046 (p-80) REVERT: B 340 ASP cc_start: 0.8418 (t0) cc_final: 0.8182 (t0) REVERT: B 354 ILE cc_start: 0.9128 (mm) cc_final: 0.8815 (mt) REVERT: C 380 MET cc_start: 0.8789 (tpp) cc_final: 0.8527 (tpp) REVERT: D 36 MET cc_start: 0.8887 (mmt) cc_final: 0.8610 (mmm) REVERT: D 138 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7218 (tt) REVERT: D 221 THR cc_start: 0.8616 (t) cc_final: 0.8316 (p) REVERT: D 274 ASN cc_start: 0.8067 (m-40) cc_final: 0.7721 (m-40) REVERT: D 340 ASP cc_start: 0.8475 (t0) cc_final: 0.8099 (t0) REVERT: F 118 ASN cc_start: 0.8233 (m-40) cc_final: 0.7910 (p0) REVERT: F 235 MET cc_start: 0.7825 (tpt) cc_final: 0.7536 (tpt) REVERT: F 340 ASP cc_start: 0.8526 (t0) cc_final: 0.8298 (t0) REVERT: G 189 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8053 (mt) outliers start: 78 outliers final: 59 residues processed: 231 average time/residue: 0.1252 time to fit residues: 51.2949 Evaluate side-chains 214 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 152 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 CYS Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain B residue 9 CYS Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 247 HIS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain C residue 9 CYS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain D residue 9 CYS Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 247 HIS Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 351 PHE Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 9 CYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 351 PHE Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 325 ASN Chi-restraints excluded: chain G residue 331 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 167 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 63 optimal weight: 20.0000 chunk 267 optimal weight: 20.0000 chunk 138 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 143 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 HIS E 110 HIS E 373 GLN F 51 HIS G 110 HIS ** G 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.079833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.073445 restraints weight = 50940.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.075657 restraints weight = 21213.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.076987 restraints weight = 10918.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.077800 restraints weight = 6442.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.078336 restraints weight = 4177.977| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.256 23849 Z= 0.131 Angle : 0.757 14.244 32893 Z= 0.320 Chirality : 0.043 0.167 3157 Planarity : 0.004 0.046 4179 Dihedral : 14.790 89.805 3430 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.39 % Favored : 88.36 % Rotamer: Outliers : 3.39 % Allowed : 14.15 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.16), residues: 2835 helix: -0.21 (0.30), residues: 336 sheet: None (None), residues: 0 loop : -1.67 (0.13), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 344 TYR 0.013 0.001 TYR F 150 PHE 0.010 0.001 PHE A 351 TRP 0.024 0.002 TRP D 238 HIS 0.005 0.001 HIS D 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.13 (23730) covalent geometry : angle 0.75734 / 0.32 (32893) hydrogen bonds : bond 0.02511 / 1.76 ( 252) hydrogen bonds : angle 4.38732 / 2.88 ( 504) Misc. bond : bond 0.07175 / 4.85 ( 119) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 188 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: A 342 MET cc_start: 0.8971 (tpp) cc_final: 0.8379 (ttm) REVERT: B 85 ASP cc_start: 0.7726 (m-30) cc_final: 0.7291 (m-30) REVERT: B 340 ASP cc_start: 0.8346 (t0) cc_final: 0.8037 (t0) REVERT: B 354 ILE cc_start: 0.9128 (mm) cc_final: 0.8835 (mt) REVERT: C 380 MET cc_start: 0.8841 (tpp) cc_final: 0.8597 (tpp) REVERT: D 36 MET cc_start: 0.8930 (mmt) cc_final: 0.8619 (mmm) REVERT: D 85 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7481 (m-30) REVERT: D 221 THR cc_start: 0.8620 (t) cc_final: 0.8271 (p) REVERT: D 274 ASN cc_start: 0.8000 (m-40) cc_final: 0.7657 (m-40) REVERT: D 340 ASP cc_start: 0.8380 (t0) cc_final: 0.8053 (t0) REVERT: E 189 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8019 (mt) REVERT: E 337 SER cc_start: 0.8647 (m) cc_final: 0.7969 (p) REVERT: F 340 ASP cc_start: 0.8442 (t0) cc_final: 0.8134 (t0) REVERT: G 85 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.7185 (m-30) REVERT: G 138 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7464 (tp) REVERT: G 149 LYS cc_start: 0.8230 (mttt) cc_final: 0.7779 (mmtt) REVERT: G 189 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7969 (mt) outliers start: 74 outliers final: 56 residues processed: 240 average time/residue: 0.1289 time to fit residues: 54.7514 Evaluate side-chains 226 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 165 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 CYS Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 9 CYS Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain C residue 9 CYS Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 325 ASN Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain D residue 9 CYS Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 247 HIS Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain D residue 403 CYS Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 9 CYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 312 ILE Chi-restraints excluded: chain F residue 351 PHE Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 325 ASN Chi-restraints excluded: chain G residue 331 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 229 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 251 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 71 optimal weight: 30.0000 chunk 175 optimal weight: 0.7980 chunk 243 optimal weight: 0.0970 chunk 96 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 190 optimal weight: 20.0000 chunk 147 optimal weight: 20.0000 overall best weight: 3.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 HIS ** D 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.078750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.072355 restraints weight = 50821.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.074564 restraints weight = 21205.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.075892 restraints weight = 10927.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.076712 restraints weight = 6464.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.077245 restraints weight = 4193.245| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.223 23849 Z= 0.155 Angle : 0.784 15.579 32893 Z= 0.326 Chirality : 0.044 0.168 3157 Planarity : 0.004 0.047 4179 Dihedral : 14.875 89.914 3430 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.18 % Favored : 88.57 % Rotamer: Outliers : 3.94 % Allowed : 14.24 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.16), residues: 2835 helix: -0.23 (0.30), residues: 336 sheet: None (None), residues: 0 loop : -1.65 (0.13), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 333 TYR 0.014 0.001 TYR F 150 PHE 0.012 0.002 PHE B 86 TRP 0.027 0.002 TRP D 238 HIS 0.006 0.001 HIS A 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.15 (23730) covalent geometry : angle 0.78444 / 0.33 (32893) hydrogen bonds : bond 0.02521 / 1.77 ( 252) hydrogen bonds : angle 4.44920 / 2.92 ( 504) Misc. bond : bond 0.08076 / 5.41 ( 119) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 173 time to evaluate : 0.840 Fit side-chains REVERT: A 342 MET cc_start: 0.8885 (tpp) cc_final: 0.8403 (ttm) REVERT: B 85 ASP cc_start: 0.7891 (m-30) cc_final: 0.7420 (m-30) REVERT: B 247 HIS cc_start: 0.8777 (OUTLIER) cc_final: 0.8052 (p-80) REVERT: B 340 ASP cc_start: 0.8353 (t0) cc_final: 0.8036 (t0) REVERT: B 354 ILE cc_start: 0.9133 (mm) cc_final: 0.8821 (mt) REVERT: C 380 MET cc_start: 0.8848 (tpp) cc_final: 0.8605 (tpp) REVERT: D 36 MET cc_start: 0.8801 (mmt) cc_final: 0.8543 (mmm) REVERT: D 85 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7557 (m-30) REVERT: D 221 THR cc_start: 0.8538 (t) cc_final: 0.8246 (p) REVERT: D 274 ASN cc_start: 0.8088 (m-40) cc_final: 0.7847 (m-40) REVERT: D 340 ASP cc_start: 0.8414 (t0) cc_final: 0.7967 (t0) REVERT: E 138 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7271 (tp) REVERT: E 189 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8088 (mt) REVERT: E 337 SER cc_start: 0.8733 (m) cc_final: 0.8095 (p) REVERT: F 235 MET cc_start: 0.7806 (tpt) cc_final: 0.7517 (tpt) REVERT: F 340 ASP cc_start: 0.8487 (t0) cc_final: 0.8179 (t0) REVERT: G 85 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7304 (m-30) REVERT: G 138 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7453 (tp) REVERT: G 149 LYS cc_start: 0.8283 (mttt) cc_final: 0.7801 (mmtt) REVERT: G 189 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8059 (mt) outliers start: 86 outliers final: 66 residues processed: 233 average time/residue: 0.1285 time to fit residues: 52.4281 Evaluate side-chains 230 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 157 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 CYS Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 9 CYS Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 247 HIS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 403 CYS Chi-restraints excluded: chain C residue 9 CYS Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 403 CYS Chi-restraints excluded: chain D residue 9 CYS Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 247 HIS Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain D residue 403 CYS Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 247 HIS Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 9 CYS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 351 PHE Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 325 ASN Chi-restraints excluded: chain G residue 331 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 58 optimal weight: 7.9990 chunk 272 optimal weight: 0.3980 chunk 116 optimal weight: 0.0000 chunk 251 optimal weight: 6.9990 chunk 240 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 212 optimal weight: 8.9990 chunk 172 optimal weight: 9.9990 chunk 266 optimal weight: 9.9990 chunk 173 optimal weight: 30.0000 chunk 170 optimal weight: 6.9990 overall best weight: 3.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN B 325 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.078375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.071850 restraints weight = 51278.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.074076 restraints weight = 21702.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.075409 restraints weight = 11323.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.076252 restraints weight = 6746.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.076784 restraints weight = 4392.549| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.215 23849 Z= 0.161 Angle : 0.791 15.797 32893 Z= 0.329 Chirality : 0.044 0.169 3157 Planarity : 0.004 0.050 4179 Dihedral : 14.911 89.787 3430 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.53 % Favored : 88.22 % Rotamer: Outliers : 3.80 % Allowed : 14.33 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.16), residues: 2835 helix: -0.24 (0.30), residues: 336 sheet: None (None), residues: 0 loop : -1.64 (0.13), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 333 TYR 0.014 0.001 TYR F 150 PHE 0.012 0.002 PHE B 86 TRP 0.027 0.002 TRP D 238 HIS 0.006 0.001 HIS A 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.16 (23730) covalent geometry : angle 0.79149 / 0.33 (32893) hydrogen bonds : bond 0.02523 / 1.77 ( 252) hydrogen bonds : angle 4.47714 / 2.93 ( 504) Misc. bond : bond 0.08177 / 5.47 ( 119) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 162 time to evaluate : 0.862 Fit side-chains REVERT: A 342 MET cc_start: 0.8885 (tpp) cc_final: 0.8426 (ttm) REVERT: B 85 ASP cc_start: 0.7902 (m-30) cc_final: 0.7435 (m-30) REVERT: B 247 HIS cc_start: 0.8806 (OUTLIER) cc_final: 0.8052 (p-80) REVERT: B 340 ASP cc_start: 0.8367 (t0) cc_final: 0.8048 (t0) REVERT: C 380 MET cc_start: 0.8853 (tpp) cc_final: 0.8617 (tpp) REVERT: D 36 MET cc_start: 0.8840 (mmt) cc_final: 0.8540 (mmm) REVERT: D 85 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7549 (m-30) REVERT: D 221 THR cc_start: 0.8561 (t) cc_final: 0.8275 (p) REVERT: D 340 ASP cc_start: 0.8426 (t0) cc_final: 0.7919 (t0) REVERT: E 138 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7303 (tp) REVERT: E 189 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8109 (mt) REVERT: F 235 MET cc_start: 0.7793 (tpt) cc_final: 0.7531 (tpt) REVERT: F 340 ASP cc_start: 0.8428 (t0) cc_final: 0.8165 (t0) REVERT: G 85 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7348 (m-30) REVERT: G 138 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7463 (tp) REVERT: G 189 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8084 (mt) outliers start: 83 outliers final: 68 residues processed: 218 average time/residue: 0.1261 time to fit residues: 49.0364 Evaluate side-chains 235 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 160 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 CYS Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 9 CYS Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 247 HIS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 403 CYS Chi-restraints excluded: chain C residue 9 CYS Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 403 CYS Chi-restraints excluded: chain D residue 9 CYS Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 247 HIS Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain D residue 403 CYS Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 247 HIS Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 351 PHE Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 9 CYS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 351 PHE Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 325 ASN Chi-restraints excluded: chain G residue 331 CYS Chi-restraints excluded: chain G residue 351 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 164 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 chunk 136 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 274 optimal weight: 10.0000 chunk 210 optimal weight: 20.0000 chunk 237 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 31 optimal weight: 30.0000 chunk 21 optimal weight: 9.9990 overall best weight: 9.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN A 325 ASN A 373 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 286 GLN ** G 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 404 HIS ** 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 = 0.2895 r_free = 0.2895 target = 0.073038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.066549 restraints weight = 52361.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.068701 restraints weight = 21851.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.070015 restraints weight = 11426.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.070833 restraints weight = 6888.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.071369 restraints weight = 4581.787| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.407 23849 Z= 0.302 Angle : 0.982 19.753 32893 Z= 0.402 Chirality : 0.048 0.182 3157 Planarity : 0.005 0.050 4179 Dihedral : 15.592 89.678 3430 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.25 % Allowed : 14.04 % Favored : 85.71 % Rotamer: Outliers : 3.39 % Allowed : 14.93 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.16), residues: 2835 helix: -0.62 (0.29), residues: 336 sheet: None (None), residues: 0 loop : -1.76 (0.13), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 220 TYR 0.020 0.002 TYR B 150 PHE 0.025 0.003 PHE B 86 TRP 0.030 0.003 TRP C 238 HIS 0.009 0.002 HIS A 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00798 / 0.29 (23730) covalent geometry : angle 0.98188 / 0.40 (32893) hydrogen bonds : bond 0.03114 / 2.15 ( 252) hydrogen bonds : angle 5.06962 / 3.34 ( 504) Misc. bond : bond 0.14733 / 10.24 ( 119) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 153 time to evaluate : 0.831 Fit side-chains REVERT: A 342 MET cc_start: 0.8904 (tpp) cc_final: 0.8378 (ttm) REVERT: B 85 ASP cc_start: 0.8107 (m-30) cc_final: 0.7569 (m-30) REVERT: B 247 HIS cc_start: 0.8925 (OUTLIER) cc_final: 0.7945 (p-80) REVERT: C 85 ASP cc_start: 0.8195 (m-30) cc_final: 0.7615 (m-30) REVERT: D 36 MET cc_start: 0.8874 (mmt) cc_final: 0.8638 (mmm) REVERT: D 85 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7762 (m-30) REVERT: D 221 THR cc_start: 0.8674 (t) cc_final: 0.8220 (p) REVERT: E 138 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7324 (tp) REVERT: F 118 ASN cc_start: 0.8338 (m-40) cc_final: 0.8054 (p0) REVERT: F 235 MET cc_start: 0.7815 (tpt) cc_final: 0.7440 (tpt) REVERT: G 85 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7312 (t70) REVERT: G 138 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7469 (tp) REVERT: G 314 ASP cc_start: 0.7507 (m-30) cc_final: 0.7282 (p0) outliers start: 74 outliers final: 64 residues processed: 212 average time/residue: 0.1301 time to fit residues: 48.6738 Evaluate side-chains 212 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 143 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 CYS Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 351 PHE Chi-restraints excluded: chain B residue 9 CYS Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 247 HIS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain C residue 9 CYS Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain D residue 9 CYS Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 247 HIS Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 351 PHE Chi-restraints excluded: chain E residue 9 CYS Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 247 HIS Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 351 PHE Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 390 ASP Chi-restraints excluded: chain F residue 9 CYS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 351 PHE Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 85 ASP Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 189 LEU Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 325 ASN Chi-restraints excluded: chain G residue 331 CYS Chi-restraints excluded: chain G residue 351 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 212 optimal weight: 20.0000 chunk 273 optimal weight: 0.6980 chunk 65 optimal weight: 50.0000 chunk 143 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 221 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 139 optimal weight: 10.0000 chunk 243 optimal weight: 0.9980 chunk 231 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN B 325 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 404 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.078800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.072309 restraints weight = 51200.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.074523 restraints weight = 21413.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.075856 restraints weight = 11107.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.076688 restraints weight = 6617.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.077216 restraints weight = 4328.686| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.201 23849 Z= 0.139 Angle : 0.779 14.819 32893 Z= 0.332 Chirality : 0.044 0.169 3157 Planarity : 0.004 0.057 4179 Dihedral : 14.991 89.527 3430 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.34 % Favored : 89.42 % Rotamer: Outliers : 3.39 % Allowed : 15.02 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.16), residues: 2835 helix: -0.28 (0.30), residues: 336 sheet: None (None), residues: 0 loop : -1.62 (0.13), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 107 TYR 0.012 0.001 TYR B 150 PHE 0.011 0.001 PHE A 351 TRP 0.030 0.002 TRP D 238 HIS 0.006 0.001 HIS D 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.14 (23730) covalent geometry : angle 0.77926 / 0.33 (32893) hydrogen bonds : bond 0.02609 / 1.82 ( 252) hydrogen bonds : angle 4.56133 / 2.98 ( 504) Misc. bond : bond 0.07482 / 4.90 ( 119) =============================================================================== Job complete usr+sys time: 3093.81 seconds wall clock time: 55 minutes 17.39 seconds (3317.39 seconds total)