Starting phenix.real_space_refine on Wed Aug 5 18:33:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ypo_34010/08_2026/7ypo_34010.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ypo_34010/08_2026/7ypo_34010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ypo_34010/08_2026/7ypo_34010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ypo_34010/08_2026/7ypo_34010.map" model { file = "/net/cci-nas-00/data/ceres_data/7ypo_34010/08_2026/7ypo_34010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ypo_34010/08_2026/7ypo_34010.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.111 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 P 28 5.49 5 S 48 5.16 5 C 7084 2.51 5 N 1892 2.21 5 O 2272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11324 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2684 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 324} Chain breaks: 1 Chain: "B" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2684 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 324} Chain breaks: 1 Chain: "C" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2684 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 324} Chain breaks: 1 Chain: "D" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2684 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 324} Chain breaks: 1 Chain: "Q" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 588 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Time building chain proxies: 2.49, per 1000 atoms: 0.22 Number of scatterers: 11324 At special positions: 0 Unit cell: (114, 109.25, 125.4, 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) S 48 16.00 P 28 15.00 O 2272 8.00 N 1892 7.00 C 7084 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 440.3 milliseconds 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2536 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 24 sheets defined 18.3% alpha, 41.9% beta 0 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 88 through 95 Processing helix chain 'A' and resid 135 through 141 Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 203 through 213 Processing helix chain 'A' and resid 319 through 343 removed outlier: 3.543A pdb=" N ASP A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 95 Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'B' and resid 188 through 196 Processing helix chain 'B' and resid 203 through 213 Processing helix chain 'B' and resid 319 through 343 removed outlier: 3.542A pdb=" N ASP B 324 " --> pdb=" O LYS B 320 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN B 338 " --> pdb=" O LEU B 334 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 95 Processing helix chain 'C' and resid 135 through 141 Processing helix chain 'C' and resid 188 through 196 Processing helix chain 'C' and resid 203 through 213 Processing helix chain 'C' and resid 319 through 343 removed outlier: 3.542A pdb=" N ASP C 324 " --> pdb=" O LYS C 320 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN C 338 " --> pdb=" O LEU C 334 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER C 339 " --> pdb=" O SER C 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 95 Processing helix chain 'D' and resid 135 through 141 Processing helix chain 'D' and resid 188 through 196 Processing helix chain 'D' and resid 203 through 213 Processing helix chain 'D' and resid 319 through 343 removed outlier: 3.542A pdb=" N ASP D 324 " --> pdb=" O LYS D 320 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN D 338 " --> pdb=" O LEU D 334 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER D 339 " --> pdb=" O SER D 335 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 87 removed outlier: 4.247A pdb=" N TYR A 72 " --> pdb=" O GLY A 87 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLU A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER A 65 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TYR A 71 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR A 63 " --> pdb=" O TYR A 71 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU A 73 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LYS A 61 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LYS A 75 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLU A 102 " --> pdb=" O TYR A 117 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TYR A 117 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL A 104 " --> pdb=" O LYS A 115 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 134 removed outlier: 6.392A pdb=" N VAL A 133 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 133 through 134 removed outlier: 6.392A pdb=" N VAL A 133 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LYS A 164 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLY A 153 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL A 166 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU A 170 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N LEU A 147 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 11.540A pdb=" N GLU A 172 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 14.796A pdb=" N SER A 145 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LYS A 144 " --> pdb=" O ARG A 223 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE A 224 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 10.189A pdb=" N ASN A 241 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 228 Processing sheet with id=AA5, first strand: chain 'A' and resid 272 through 277 removed outlier: 5.717A pdb=" N VAL A 353 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE A 364 " --> pdb=" O VAL A 353 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 282 through 288 Processing sheet with id=AA7, first strand: chain 'B' and resid 81 through 87 removed outlier: 4.247A pdb=" N TYR B 72 " --> pdb=" O GLY B 87 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLU B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER B 65 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TYR B 71 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR B 63 " --> pdb=" O TYR B 71 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU B 73 " --> pdb=" O LYS B 61 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS B 61 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LYS B 75 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLU B 102 " --> pdb=" O TYR B 117 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR B 117 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL B 104 " --> pdb=" O LYS B 115 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 133 through 134 removed outlier: 6.392A pdb=" N VAL B 133 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 133 through 134 removed outlier: 6.392A pdb=" N VAL B 133 " --> pdb=" O GLU B 172 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LYS B 164 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLY B 153 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL B 166 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU B 170 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N LEU B 147 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 11.540A pdb=" N GLU B 172 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 14.796A pdb=" N SER B 145 " --> pdb=" O GLU B 172 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LYS B 144 " --> pdb=" O ARG B 223 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE B 224 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N ASN B 241 " --> pdb=" O ILE B 224 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 227 through 228 Processing sheet with id=AB2, first strand: chain 'B' and resid 272 through 277 removed outlier: 5.716A pdb=" N VAL B 353 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE B 364 " --> pdb=" O VAL B 353 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 282 through 288 Processing sheet with id=AB4, first strand: chain 'C' and resid 81 through 87 removed outlier: 4.246A pdb=" N TYR C 72 " --> pdb=" O GLY C 87 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLU C 69 " --> pdb=" O SER C 65 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER C 65 " --> pdb=" O GLU C 69 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TYR C 71 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR C 63 " --> pdb=" O TYR C 71 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU C 73 " --> pdb=" O LYS C 61 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS C 61 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LYS C 75 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLU C 102 " --> pdb=" O TYR C 117 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TYR C 117 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL C 104 " --> pdb=" O LYS C 115 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 133 through 134 removed outlier: 6.392A pdb=" N VAL C 133 " --> pdb=" O GLU C 172 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 133 through 134 removed outlier: 6.392A pdb=" N VAL C 133 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LYS C 164 " --> pdb=" O GLY C 153 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLY C 153 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL C 166 " --> pdb=" O LEU C 151 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU C 170 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N LEU C 147 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 11.540A pdb=" N GLU C 172 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 14.796A pdb=" N SER C 145 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LYS C 144 " --> pdb=" O ARG C 223 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE C 224 " --> pdb=" O ASN C 241 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N ASN C 241 " --> pdb=" O ILE C 224 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 227 through 228 Processing sheet with id=AB8, first strand: chain 'C' and resid 272 through 277 removed outlier: 5.716A pdb=" N VAL C 353 " --> pdb=" O ILE C 364 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE C 364 " --> pdb=" O VAL C 353 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 282 through 288 Processing sheet with id=AC1, first strand: chain 'D' and resid 81 through 87 removed outlier: 4.246A pdb=" N TYR D 72 " --> pdb=" O GLY D 87 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLU D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER D 65 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TYR D 71 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR D 63 " --> pdb=" O TYR D 71 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU D 73 " --> pdb=" O LYS D 61 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS D 61 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LYS D 75 " --> pdb=" O LEU D 59 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLU D 102 " --> pdb=" O TYR D 117 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TYR D 117 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL D 104 " --> pdb=" O LYS D 115 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 133 through 134 removed outlier: 6.392A pdb=" N VAL D 133 " --> pdb=" O GLU D 172 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 133 through 134 removed outlier: 6.392A pdb=" N VAL D 133 " --> pdb=" O GLU D 172 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LYS D 164 " --> pdb=" O GLY D 153 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLY D 153 " --> pdb=" O LYS D 164 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL D 166 " --> pdb=" O LEU D 151 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU D 170 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N LEU D 147 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 11.540A pdb=" N GLU D 172 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 14.796A pdb=" N SER D 145 " --> pdb=" O GLU D 172 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LYS D 144 " --> pdb=" O ARG D 223 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE D 224 " --> pdb=" O ASN D 241 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N ASN D 241 " --> pdb=" O ILE D 224 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 227 through 228 Processing sheet with id=AC5, first strand: chain 'D' and resid 272 through 277 removed outlier: 5.717A pdb=" N VAL D 353 " --> pdb=" O ILE D 364 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE D 364 " --> pdb=" O VAL D 353 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 282 through 288 416 hydrogen bonds defined for protein. 1188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 1.28 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3607 1.34 - 1.46: 2568 1.46 - 1.57: 5273 1.57 - 1.69: 55 1.69 - 1.81: 76 Bond restraints: 11579 Sorted by residual: bond pdb=" C3' DA Q 26 " pdb=" C2' DA Q 26 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.83e+00 bond pdb=" C3' DA Q 12 " pdb=" C2' DA Q 12 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.10e+00 bond pdb=" C3' DA Q 11 " pdb=" O3' DA Q 11 " ideal model delta sigma weight residual 1.435 1.401 0.034 1.30e-02 5.92e+03 6.66e+00 bond pdb=" C3' DA Q 21 " pdb=" C2' DA Q 21 " ideal model delta sigma weight residual 1.516 1.532 -0.016 8.00e-03 1.56e+04 4.08e+00 bond pdb=" C4' DA Q 25 " pdb=" C3' DA Q 25 " ideal model delta sigma weight residual 1.529 1.510 0.019 1.00e-02 1.00e+04 3.56e+00 ... (remaining 11574 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 14875 1.21 - 2.42: 748 2.42 - 3.63: 100 3.63 - 4.83: 17 4.83 - 6.04: 4 Bond angle restraints: 15744 Sorted by residual: angle pdb=" O4' DA Q 25 " pdb=" C4' DA Q 25 " pdb=" C3' DA Q 25 " ideal model delta sigma weight residual 106.00 103.84 2.16 6.00e-01 2.78e+00 1.30e+01 angle pdb=" O4' DA Q 24 " pdb=" C4' DA Q 24 " pdb=" C3' DA Q 24 " ideal model delta sigma weight residual 106.00 104.01 1.99 6.00e-01 2.78e+00 1.10e+01 angle pdb=" C ARG B 109 " pdb=" N LYS B 110 " pdb=" CA LYS B 110 " ideal model delta sigma weight residual 121.54 127.58 -6.04 1.91e+00 2.74e-01 1.00e+01 angle pdb=" C ARG A 109 " pdb=" N LYS A 110 " pdb=" CA LYS A 110 " ideal model delta sigma weight residual 121.54 127.56 -6.02 1.91e+00 2.74e-01 9.92e+00 angle pdb=" C ARG D 109 " pdb=" N LYS D 110 " pdb=" CA LYS D 110 " ideal model delta sigma weight residual 121.54 127.55 -6.01 1.91e+00 2.74e-01 9.90e+00 ... (remaining 15739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.29: 6569 28.29 - 56.59: 406 56.59 - 84.88: 25 84.88 - 113.17: 4 113.17 - 141.46: 1 Dihedral angle restraints: 7005 sinusoidal: 3077 harmonic: 3928 Sorted by residual: dihedral pdb=" C4' DA Q 17 " pdb=" C3' DA Q 17 " pdb=" O3' DA Q 17 " pdb=" P DA Q 18 " ideal model delta sinusoidal sigma weight residual 220.00 78.54 141.46 1 3.50e+01 8.16e-04 1.40e+01 dihedral pdb=" CA ASN D 303 " pdb=" C ASN D 303 " pdb=" N GLU D 304 " pdb=" CA GLU D 304 " ideal model delta harmonic sigma weight residual -180.00 -162.39 -17.61 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ASN C 303 " pdb=" C ASN C 303 " pdb=" N GLU C 304 " pdb=" CA GLU C 304 " ideal model delta harmonic sigma weight residual -180.00 -162.40 -17.60 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 7002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1012 0.029 - 0.059: 441 0.059 - 0.088: 188 0.088 - 0.117: 102 0.117 - 0.147: 29 Chirality restraints: 1772 Sorted by residual: chirality pdb=" CA ILE B 83 " pdb=" N ILE B 83 " pdb=" C ILE B 83 " pdb=" CB ILE B 83 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.38e-01 chirality pdb=" CA ILE A 83 " pdb=" N ILE A 83 " pdb=" C ILE A 83 " pdb=" CB ILE A 83 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA ILE D 83 " pdb=" N ILE D 83 " pdb=" C ILE D 83 " pdb=" CB ILE D 83 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.25e-01 ... (remaining 1769 not shown) Planarity restraints: 1908 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 152 " -0.007 2.00e-02 2.50e+03 6.35e-03 8.06e-01 pdb=" CG TYR B 152 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR B 152 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 152 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 152 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 152 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 152 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 152 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 152 " -0.007 2.00e-02 2.50e+03 6.15e-03 7.58e-01 pdb=" CG TYR A 152 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR A 152 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 152 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 152 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 152 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 152 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 152 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 152 " 0.007 2.00e-02 2.50e+03 6.09e-03 7.42e-01 pdb=" CG TYR D 152 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR D 152 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR D 152 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR D 152 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR D 152 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 152 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 152 " 0.001 2.00e-02 2.50e+03 ... (remaining 1905 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 172 2.65 - 3.21: 10736 3.21 - 3.78: 16580 3.78 - 4.34: 23545 4.34 - 4.90: 38894 Nonbonded interactions: 89927 Sorted by model distance: nonbonded pdb=" OD1 ASP D 188 " pdb=" N PHE D 189 " model vdw 2.091 3.120 nonbonded pdb=" OD1 ASP C 188 " pdb=" N PHE C 189 " model vdw 2.091 3.120 nonbonded pdb=" OD1 ASP B 188 " pdb=" N PHE B 189 " model vdw 2.091 3.120 nonbonded pdb=" OD1 ASP A 188 " pdb=" N PHE A 189 " model vdw 2.091 3.120 nonbonded pdb=" NE2 GLN A 119 " pdb=" O CYS A 120 " model vdw 2.241 3.120 ... (remaining 89922 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.000 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: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.060 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11579 Z= 0.237 Angle : 0.600 6.042 15744 Z= 0.376 Chirality : 0.045 0.147 1772 Planarity : 0.002 0.016 1908 Dihedral : 16.334 141.464 4469 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.23), residues: 1292 helix: 0.22 (0.32), residues: 248 sheet: -1.46 (0.21), residues: 504 loop : -1.43 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 223 TYR 0.016 0.001 TYR B 152 PHE 0.014 0.001 PHE A 295 HIS 0.007 0.002 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.24 (11579) covalent geometry : angle 0.59973 / 0.38 (15744) hydrogen bonds : bond 0.11464 / 7.54 ( 416) hydrogen bonds : angle 7.40723 / 4.97 ( 1188) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 157 TYR cc_start: 0.7437 (t80) cc_final: 0.6941 (t80) REVERT: D 64 MET cc_start: 0.7941 (ptp) cc_final: 0.7728 (ptp) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.0687 time to fit residues: 25.7448 Evaluate side-chains 179 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN A 68 ASN A 119 GLN B 68 ASN B 119 GLN B 229 ASN ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN C 91 GLN C 119 GLN C 270 ASN D 68 ASN ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.179642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.142952 restraints weight = 13200.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.142956 restraints weight = 12655.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.144664 restraints weight = 11841.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.145193 restraints weight = 9611.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.145968 restraints weight = 9364.494| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 11579 Z= 0.210 Angle : 0.632 6.142 15744 Z= 0.363 Chirality : 0.047 0.171 1772 Planarity : 0.003 0.032 1908 Dihedral : 14.010 137.802 1825 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.13 % Allowed : 10.73 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.23), residues: 1292 helix: 0.45 (0.32), residues: 252 sheet: -1.63 (0.21), residues: 528 loop : -1.30 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 286 TYR 0.019 0.001 TYR D 299 PHE 0.023 0.002 PHE A 135 HIS 0.007 0.002 HIS D 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.21 (11579) covalent geometry : angle 0.63221 / 0.36 (15744) hydrogen bonds : bond 0.04278 / 2.69 ( 416) hydrogen bonds : angle 6.41238 / 4.37 ( 1188) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 194 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 TYR cc_start: 0.8304 (p90) cc_final: 0.8049 (p90) REVERT: A 313 ARG cc_start: 0.7236 (mtt90) cc_final: 0.7035 (mtt-85) REVERT: C 349 ASP cc_start: 0.7556 (m-30) cc_final: 0.7303 (m-30) outliers start: 14 outliers final: 9 residues processed: 200 average time/residue: 0.0746 time to fit residues: 22.4120 Evaluate side-chains 183 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 174 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 258 PHE Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 200 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 35 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 121 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 62 optimal weight: 0.5980 chunk 0 optimal weight: 30.0000 chunk 75 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN B 229 ASN ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 ASN ** D 98 ASN ** 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 = 0.4032 r_free = 0.4032 target = 0.183240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.145621 restraints weight = 13192.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.145063 restraints weight = 12281.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.147118 restraints weight = 11737.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.147878 restraints weight = 9248.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.148777 restraints weight = 9039.918| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11579 Z= 0.137 Angle : 0.556 10.600 15744 Z= 0.324 Chirality : 0.046 0.186 1772 Planarity : 0.003 0.018 1908 Dihedral : 13.921 138.081 1825 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.53 % Allowed : 14.19 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.45 (0.23), residues: 1292 helix: 0.63 (0.33), residues: 252 sheet: -1.34 (0.22), residues: 512 loop : -1.18 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 286 TYR 0.022 0.001 TYR D 256 PHE 0.017 0.001 PHE A 135 HIS 0.006 0.001 HIS C 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (11579) covalent geometry : angle 0.55636 / 0.32 (15744) hydrogen bonds : bond 0.03619 / 2.30 ( 416) hydrogen bonds : angle 6.00438 / 4.11 ( 1188) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 ARG cc_start: 0.7199 (mtt90) cc_final: 0.6947 (mtt-85) REVERT: B 173 ASP cc_start: 0.7763 (p0) cc_final: 0.7529 (p0) REVERT: C 72 TYR cc_start: 0.7719 (m-10) cc_final: 0.7442 (m-10) REVERT: C 349 ASP cc_start: 0.7507 (m-30) cc_final: 0.7255 (m-30) REVERT: D 93 PHE cc_start: 0.8643 (m-80) cc_final: 0.8061 (m-80) outliers start: 19 outliers final: 7 residues processed: 208 average time/residue: 0.0681 time to fit residues: 21.9032 Evaluate side-chains 186 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 179 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain D residue 62 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 63 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN A 316 ASN B 229 ASN C 91 GLN ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.166676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.132065 restraints weight = 13692.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.132931 restraints weight = 17984.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.134441 restraints weight = 14499.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.135384 restraints weight = 10910.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.136176 restraints weight = 10165.588| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11579 Z= 0.211 Angle : 0.586 6.052 15744 Z= 0.337 Chirality : 0.045 0.191 1772 Planarity : 0.003 0.019 1908 Dihedral : 14.084 138.965 1825 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.10 % Allowed : 16.61 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.23), residues: 1292 helix: 0.60 (0.33), residues: 252 sheet: -1.39 (0.22), residues: 512 loop : -1.24 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 268 TYR 0.018 0.001 TYR A 289 PHE 0.019 0.002 PHE D 295 HIS 0.005 0.001 HIS D 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.21 (11579) covalent geometry : angle 0.58619 / 0.34 (15744) hydrogen bonds : bond 0.03781 / 2.40 ( 416) hydrogen bonds : angle 5.95866 / 4.09 ( 1188) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 ARG cc_start: 0.7120 (mtt90) cc_final: 0.6845 (mtt-85) REVERT: C 72 TYR cc_start: 0.7729 (m-80) cc_final: 0.7522 (m-10) REVERT: C 117 TYR cc_start: 0.8161 (p90) cc_final: 0.7854 (p90) REVERT: C 156 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8094 (mm) REVERT: C 377 GLU cc_start: 0.8210 (tp30) cc_final: 0.7996 (tp30) REVERT: D 93 PHE cc_start: 0.8585 (m-80) cc_final: 0.7991 (m-80) outliers start: 26 outliers final: 17 residues processed: 200 average time/residue: 0.0704 time to fit residues: 21.6568 Evaluate side-chains 187 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 283 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 80 optimal weight: 0.0060 chunk 0 optimal weight: 30.0000 chunk 79 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 128 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN A 79 ASN A 316 ASN ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 ASN ** 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 = 0.3999 r_free = 0.3999 target = 0.179902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.144181 restraints weight = 13112.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.143966 restraints weight = 13330.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.145582 restraints weight = 12748.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.145980 restraints weight = 10269.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.146840 restraints weight = 10183.536| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11579 Z= 0.178 Angle : 0.552 6.693 15744 Z= 0.318 Chirality : 0.045 0.227 1772 Planarity : 0.002 0.018 1908 Dihedral : 14.272 138.502 1825 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.66 % Allowed : 17.42 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.23), residues: 1292 helix: 0.61 (0.32), residues: 252 sheet: -1.30 (0.22), residues: 512 loop : -1.17 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 313 TYR 0.017 0.001 TYR A 289 PHE 0.018 0.001 PHE A 135 HIS 0.005 0.001 HIS D 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (11579) covalent geometry : angle 0.55240 / 0.32 (15744) hydrogen bonds : bond 0.03583 / 2.27 ( 416) hydrogen bonds : angle 5.82587 / 4.00 ( 1188) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 182 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7598 (pp30) REVERT: A 313 ARG cc_start: 0.7252 (mtt90) cc_final: 0.7008 (mtt-85) REVERT: B 173 ASP cc_start: 0.7630 (p0) cc_final: 0.7407 (p0) REVERT: C 72 TYR cc_start: 0.7718 (m-80) cc_final: 0.7488 (m-10) REVERT: C 106 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7408 (pp30) REVERT: C 377 GLU cc_start: 0.8294 (tp30) cc_final: 0.7960 (tp30) REVERT: D 93 PHE cc_start: 0.8624 (m-80) cc_final: 0.8001 (m-80) REVERT: D 106 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7502 (pp30) REVERT: D 232 ASN cc_start: 0.7661 (t0) cc_final: 0.7329 (p0) outliers start: 33 outliers final: 17 residues processed: 201 average time/residue: 0.0841 time to fit residues: 25.3781 Evaluate side-chains 192 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 200 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 0.0040 chunk 75 optimal weight: 0.7980 chunk 129 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN A 67 ASN A 79 ASN ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 ASN ** 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 = 0.4031 r_free = 0.4031 target = 0.183301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.147655 restraints weight = 13103.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.147279 restraints weight = 12611.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.149292 restraints weight = 12501.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.149717 restraints weight = 9682.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.150177 restraints weight = 10071.310| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11579 Z= 0.118 Angle : 0.515 7.299 15744 Z= 0.296 Chirality : 0.044 0.182 1772 Planarity : 0.002 0.016 1908 Dihedral : 14.445 137.232 1825 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.94 % Allowed : 19.19 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.23), residues: 1292 helix: 0.66 (0.32), residues: 252 sheet: -1.26 (0.23), residues: 476 loop : -1.05 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 109 TYR 0.016 0.001 TYR A 299 PHE 0.022 0.001 PHE A 258 HIS 0.006 0.001 HIS C 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 (11579) covalent geometry : angle 0.51534 / 0.30 (15744) hydrogen bonds : bond 0.03339 / 2.13 ( 416) hydrogen bonds : angle 5.60194 / 3.85 ( 1188) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 TYR cc_start: 0.8120 (m-80) cc_final: 0.7849 (m-10) REVERT: A 106 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7698 (pt0) REVERT: B 106 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7256 (pp30) REVERT: B 173 ASP cc_start: 0.7602 (p0) cc_final: 0.7400 (p0) REVERT: C 72 TYR cc_start: 0.7647 (m-80) cc_final: 0.7440 (m-10) REVERT: C 106 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7348 (pp30) REVERT: D 106 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7432 (pp30) outliers start: 24 outliers final: 9 residues processed: 205 average time/residue: 0.0822 time to fit residues: 25.3024 Evaluate side-chains 186 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 173 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 200 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.9980 chunk 112 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 25 optimal weight: 0.0980 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.181402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.144480 restraints weight = 13151.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.144785 restraints weight = 12599.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.146330 restraints weight = 11900.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.146892 restraints weight = 9485.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.147674 restraints weight = 9212.305| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11579 Z= 0.172 Angle : 0.548 7.619 15744 Z= 0.310 Chirality : 0.045 0.175 1772 Planarity : 0.002 0.017 1908 Dihedral : 14.641 137.534 1825 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.18 % Allowed : 19.76 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.23), residues: 1292 helix: 0.66 (0.32), residues: 252 sheet: -1.27 (0.23), residues: 476 loop : -1.02 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 268 TYR 0.014 0.001 TYR D 299 PHE 0.024 0.001 PHE A 135 HIS 0.005 0.001 HIS D 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (11579) covalent geometry : angle 0.54763 / 0.31 (15744) hydrogen bonds : bond 0.03453 / 2.18 ( 416) hydrogen bonds : angle 5.59387 / 3.84 ( 1188) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7509 (pp30) REVERT: B 106 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7257 (pp30) REVERT: C 72 TYR cc_start: 0.7680 (m-80) cc_final: 0.7456 (m-10) REVERT: D 106 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7426 (pp30) outliers start: 27 outliers final: 17 residues processed: 187 average time/residue: 0.0886 time to fit residues: 24.7790 Evaluate side-chains 189 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 200 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 125 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 86 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.182665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.144935 restraints weight = 13014.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.144603 restraints weight = 12036.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.146574 restraints weight = 11613.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.147290 restraints weight = 9131.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.148147 restraints weight = 8928.230| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11579 Z= 0.145 Angle : 0.522 7.622 15744 Z= 0.296 Chirality : 0.044 0.180 1772 Planarity : 0.002 0.014 1908 Dihedral : 14.736 136.983 1825 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.77 % Allowed : 20.73 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.23), residues: 1292 helix: 0.84 (0.33), residues: 252 sheet: -1.15 (0.23), residues: 476 loop : -0.96 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 268 TYR 0.014 0.001 TYR A 299 PHE 0.016 0.001 PHE A 135 HIS 0.005 0.001 HIS B 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (11579) covalent geometry : angle 0.52164 / 0.30 (15744) hydrogen bonds : bond 0.03275 / 2.09 ( 416) hydrogen bonds : angle 5.52739 / 3.80 ( 1188) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7830 (pt0) REVERT: B 106 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7225 (pp30) REVERT: C 72 TYR cc_start: 0.7659 (m-80) cc_final: 0.7435 (m-10) REVERT: C 110 LYS cc_start: 0.7460 (tppt) cc_final: 0.7255 (tppt) REVERT: C 117 TYR cc_start: 0.7899 (p90) cc_final: 0.7649 (p90) REVERT: D 106 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7444 (pp30) outliers start: 22 outliers final: 14 residues processed: 187 average time/residue: 0.0840 time to fit residues: 23.5584 Evaluate side-chains 186 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 200 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 4 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 84 optimal weight: 20.0000 chunk 114 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN C 67 ASN ** C 361 ASN ** 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 = 0.3966 r_free = 0.3966 target = 0.176375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.140282 restraints weight = 13166.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.139785 restraints weight = 14735.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.141471 restraints weight = 13946.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.141990 restraints weight = 10860.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.142946 restraints weight = 10365.712| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 11579 Z= 0.316 Angle : 0.661 7.243 15744 Z= 0.365 Chirality : 0.047 0.178 1772 Planarity : 0.003 0.026 1908 Dihedral : 14.934 138.836 1825 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.50 % Allowed : 20.24 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.23), residues: 1292 helix: 0.58 (0.32), residues: 248 sheet: -1.24 (0.22), residues: 540 loop : -0.94 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 313 TYR 0.018 0.002 TYR C 107 PHE 0.034 0.002 PHE B 295 HIS 0.004 0.002 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00730 / 0.32 (11579) covalent geometry : angle 0.66085 / 0.36 (15744) hydrogen bonds : bond 0.04120 / 2.59 ( 416) hydrogen bonds : angle 5.95173 / 4.07 ( 1188) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: B 106 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7296 (pp30) REVERT: C 72 TYR cc_start: 0.7794 (m-80) cc_final: 0.7527 (m-10) REVERT: D 106 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.8002 (pt0) outliers start: 31 outliers final: 21 residues processed: 183 average time/residue: 0.0829 time to fit residues: 22.6587 Evaluate side-chains 184 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 200 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 6 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN A 106 GLN ** C 361 ASN ** 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 = 0.3971 r_free = 0.3971 target = 0.176900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.140632 restraints weight = 13233.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.140117 restraints weight = 14936.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.141801 restraints weight = 13844.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.142437 restraints weight = 10960.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.143377 restraints weight = 10490.546| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.166 11579 Z= 0.284 Angle : 0.889 59.199 15744 Z= 0.520 Chirality : 0.048 0.537 1772 Planarity : 0.003 0.025 1908 Dihedral : 14.933 138.769 1825 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.34 % Allowed : 20.08 % Favored : 77.58 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.23), residues: 1292 helix: 0.59 (0.32), residues: 248 sheet: -1.25 (0.22), residues: 540 loop : -0.97 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 313 TYR 0.017 0.002 TYR C 107 PHE 0.031 0.002 PHE B 295 HIS 0.004 0.001 HIS D 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.28 (11579) covalent geometry : angle 0.88902 / 0.52 (15744) hydrogen bonds : bond 0.03949 / 2.49 ( 416) hydrogen bonds : angle 5.93704 / 4.06 ( 1188) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: B 106 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7282 (pp30) REVERT: C 72 TYR cc_start: 0.7785 (m-80) cc_final: 0.7516 (m-10) REVERT: D 106 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7998 (pt0) outliers start: 29 outliers final: 23 residues processed: 176 average time/residue: 0.0979 time to fit residues: 25.7972 Evaluate side-chains 189 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 64 MET Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 245 GLU Chi-restraints excluded: chain D residue 308 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 83 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 120 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 108 optimal weight: 20.0000 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN A 106 GLN ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 ASN ** 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 = 0.4003 r_free = 0.4003 target = 0.180527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.144888 restraints weight = 13118.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.144814 restraints weight = 12956.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.146426 restraints weight = 12370.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.146767 restraints weight = 10036.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.147518 restraints weight = 9965.290| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11579 Z= 0.158 Angle : 0.568 7.587 15744 Z= 0.318 Chirality : 0.045 0.204 1772 Planarity : 0.003 0.024 1908 Dihedral : 14.852 137.852 1825 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.10 % Allowed : 20.48 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.23), residues: 1292 helix: 0.68 (0.33), residues: 252 sheet: -1.25 (0.23), residues: 496 loop : -1.04 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 313 TYR 0.016 0.001 TYR A 157 PHE 0.018 0.001 PHE A 135 HIS 0.005 0.001 HIS B 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (11579) covalent geometry : angle 0.56794 / 0.32 (15744) hydrogen bonds : bond 0.03493 / 2.23 ( 416) hydrogen bonds : angle 5.74728 / 3.94 ( 1188) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1448.49 seconds wall clock time: 26 minutes 4.55 seconds (1564.55 seconds total)