Starting phenix.real_space_refine on Fri Jul 3 00:42:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ypo_34010/07_2026/7ypo_34010.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ypo_34010/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ypo_34010/07_2026/7ypo_34010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ypo_34010/07_2026/7ypo_34010.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ypo_34010/07_2026/7ypo_34010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ypo_34010/07_2026/7ypo_34010.map" } 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-dev-6108/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: 2.38, per 1000 atoms: 0.21 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: 1.01 Conformation dependent library (CDL) restraints added in 380.9 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: 1.26 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: 1.90 Time building geometry restraints manager: 1.31 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: 14877 1.21 - 2.42: 747 2.42 - 3.63: 99 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: 0.970 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.160 Find NCS groups from input model: 0.170 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.800 ------------------------------------------------------------------------------- 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 : 0.599 6.042 15744 Z= 0.375 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 0.59896 / 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 : 0.435 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: 0.6962 (t80) REVERT: D 64 MET cc_start: 0.7941 (ptp) cc_final: 0.7729 (ptp) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.0820 time to fit residues: 30.6011 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 : 0.360 ------------------------------------------------------------------------------- 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: 6.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 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 = 0.3999 r_free = 0.3999 target = 0.179549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.142276 restraints weight = 13192.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.141633 restraints weight = 13020.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.143544 restraints weight = 12334.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.144203 restraints weight = 9859.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.145159 restraints weight = 9680.434| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 11579 Z= 0.206 Angle : 0.630 6.062 15744 Z= 0.362 Chirality : 0.047 0.185 1772 Planarity : 0.003 0.032 1908 Dihedral : 14.011 137.890 1825 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.29 % Allowed : 10.81 % Favored : 87.90 % 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: -1.77 (0.23), residues: 1292 helix: 0.46 (0.33), residues: 252 sheet: -1.63 (0.21), residues: 528 loop : -1.29 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 286 TYR 0.018 0.001 TYR D 299 PHE 0.023 0.002 PHE A 135 HIS 0.006 0.002 HIS D 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.21 (11579) covalent geometry : angle 0.63032 / 0.36 (15744) hydrogen bonds : bond 0.04291 / 2.71 ( 416) hydrogen bonds : angle 6.39850 / 4.36 ( 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 211 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 195 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 TYR cc_start: 0.8217 (p90) cc_final: 0.7978 (p90) REVERT: C 349 ASP cc_start: 0.7432 (m-30) cc_final: 0.7206 (m-30) REVERT: D 186 MET cc_start: 0.7835 (mtm) cc_final: 0.7559 (mtm) outliers start: 16 outliers final: 11 residues processed: 203 average time/residue: 0.0862 time to fit residues: 26.0151 Evaluate side-chains 183 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 172 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 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 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: 0.9980 chunk 66 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 62 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 75 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 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 = 0.4016 r_free = 0.4016 target = 0.181577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.144421 restraints weight = 13198.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.145086 restraints weight = 12180.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.146610 restraints weight = 11631.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.147121 restraints weight = 9375.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.147675 restraints weight = 9288.894| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 11579 Z= 0.156 Angle : 0.567 11.412 15744 Z= 0.330 Chirality : 0.046 0.176 1772 Planarity : 0.003 0.029 1908 Dihedral : 13.965 138.667 1825 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.85 % Allowed : 14.52 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.23), residues: 1292 helix: 0.62 (0.33), residues: 252 sheet: -1.41 (0.22), residues: 512 loop : -1.23 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 313 TYR 0.015 0.001 TYR D 256 PHE 0.019 0.001 PHE A 258 HIS 0.006 0.001 HIS D 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (11579) covalent geometry : angle 0.56696 / 0.33 (15744) hydrogen bonds : bond 0.03725 / 2.37 ( 416) hydrogen bonds : angle 6.06155 / 4.15 ( 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 208 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 ASP cc_start: 0.7743 (p0) cc_final: 0.7509 (p0) REVERT: C 72 TYR cc_start: 0.7747 (m-10) cc_final: 0.7465 (m-10) REVERT: C 117 TYR cc_start: 0.8305 (p90) cc_final: 0.7708 (p90) REVERT: C 349 ASP cc_start: 0.7526 (m-30) cc_final: 0.7285 (m-30) REVERT: D 93 PHE cc_start: 0.8639 (m-80) cc_final: 0.8022 (m-80) REVERT: D 186 MET cc_start: 0.7810 (mtm) cc_final: 0.7475 (mtm) outliers start: 23 outliers final: 11 residues processed: 200 average time/residue: 0.0853 time to fit residues: 25.7547 Evaluate side-chains 188 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 177 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 288 ILE Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 185 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 Chi-restraints excluded: chain D residue 70 ASP 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: 5.9990 chunk 42 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 39 optimal weight: 20.0000 chunk 111 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN A 316 ASN B 229 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 = 0.4006 r_free = 0.4006 target = 0.180423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.143358 restraints weight = 13162.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.143420 restraints weight = 13473.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.145214 restraints weight = 12537.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.145940 restraints weight = 9830.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.146923 restraints weight = 9411.129| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 11579 Z= 0.247 Angle : 0.620 6.312 15744 Z= 0.354 Chirality : 0.047 0.202 1772 Planarity : 0.003 0.022 1908 Dihedral : 14.135 139.856 1825 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.06 % Allowed : 16.37 % Favored : 80.56 % 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: -1.67 (0.23), residues: 1292 helix: 0.47 (0.32), residues: 252 sheet: -1.48 (0.22), residues: 512 loop : -1.33 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 286 TYR 0.016 0.001 TYR A 289 PHE 0.023 0.002 PHE C 295 HIS 0.005 0.001 HIS D 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.25 (11579) covalent geometry : angle 0.61994 / 0.35 (15744) hydrogen bonds : bond 0.04024 / 2.55 ( 416) hydrogen bonds : angle 6.07765 / 4.17 ( 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 217 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 TYR cc_start: 0.7236 (t80) cc_final: 0.7025 (t80) REVERT: C 72 TYR cc_start: 0.7790 (m-80) cc_final: 0.7541 (m-10) REVERT: C 156 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8200 (mm) REVERT: D 93 PHE cc_start: 0.8655 (m-80) cc_final: 0.8009 (m-80) REVERT: D 186 MET cc_start: 0.7818 (mtm) cc_final: 0.7561 (mtm) outliers start: 38 outliers final: 24 residues processed: 199 average time/residue: 0.0901 time to fit residues: 26.9439 Evaluate side-chains 193 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 168 VAL Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 168 VAL 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 70 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 200 VAL 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: 0.0170 chunk 0 optimal weight: 30.0000 chunk 79 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 128 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.7624 ------------------------------------------------------------------------------- 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 = 0.4001 r_free = 0.4001 target = 0.180224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.144154 restraints weight = 13084.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.142914 restraints weight = 13081.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.144742 restraints weight = 12626.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.145187 restraints weight = 10176.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.145753 restraints weight = 10391.113| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2078 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= 0.161 Angle : 0.554 6.717 15744 Z= 0.319 Chirality : 0.045 0.227 1772 Planarity : 0.002 0.017 1908 Dihedral : 14.262 138.816 1825 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.74 % Allowed : 18.06 % Favored : 79.19 % 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: -1.58 (0.23), residues: 1292 helix: 0.62 (0.33), residues: 252 sheet: -1.49 (0.23), residues: 476 loop : -1.28 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 313 TYR 0.015 0.001 TYR A 299 PHE 0.018 0.001 PHE A 258 HIS 0.005 0.001 HIS C 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (11579) covalent geometry : angle 0.55404 / 0.32 (15744) hydrogen bonds : bond 0.03554 / 2.25 ( 416) hydrogen bonds : angle 5.83349 / 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: 34 poor density : 181 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7567 (pp30) REVERT: C 72 TYR cc_start: 0.7734 (m-80) cc_final: 0.7475 (m-10) REVERT: C 106 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7423 (pp30) REVERT: C 273 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.8068 (mt) REVERT: D 106 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7498 (pp30) REVERT: D 186 MET cc_start: 0.7782 (mtm) cc_final: 0.7454 (mtm) outliers start: 34 outliers final: 14 residues processed: 201 average time/residue: 0.0889 time to fit residues: 26.5403 Evaluate side-chains 188 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 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 156 ILE Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 70 ASP 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: 5.9990 chunk 75 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN A 67 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.178498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.142530 restraints weight = 13202.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.142225 restraints weight = 13744.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.143833 restraints weight = 13092.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.144254 restraints weight = 10494.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.145018 restraints weight = 10478.300| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11579 Z= 0.196 Angle : 0.577 7.830 15744 Z= 0.328 Chirality : 0.046 0.185 1772 Planarity : 0.003 0.017 1908 Dihedral : 14.490 138.922 1825 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.31 % Allowed : 18.31 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.23), residues: 1292 helix: 0.38 (0.32), residues: 252 sheet: -1.63 (0.24), residues: 436 loop : -1.18 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 313 TYR 0.018 0.001 TYR A 289 PHE 0.031 0.002 PHE C 135 HIS 0.005 0.001 HIS D 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.20 (11579) covalent geometry : angle 0.57730 / 0.33 (15744) hydrogen bonds : bond 0.03704 / 2.35 ( 416) hydrogen bonds : angle 5.84385 / 4.01 ( 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 222 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7579 (pp30) REVERT: B 81 LYS cc_start: 0.8149 (mtpp) cc_final: 0.7806 (tttp) REVERT: B 106 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7821 (pt0) REVERT: C 72 TYR cc_start: 0.7724 (m-80) cc_final: 0.7477 (m-10) REVERT: C 106 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7415 (pp30) REVERT: C 156 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8203 (mm) REVERT: D 106 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7964 (pt0) REVERT: D 186 MET cc_start: 0.7802 (mtm) cc_final: 0.7494 (mtm) outliers start: 41 outliers final: 24 residues processed: 208 average time/residue: 0.0959 time to fit residues: 29.6647 Evaluate side-chains 197 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 106 GLN Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 266 ILE 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 70 ASP Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 308 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.181588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.144733 restraints weight = 13121.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.145066 restraints weight = 12109.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.146683 restraints weight = 11401.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.147196 restraints weight = 9326.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.147840 restraints weight = 9133.377| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11579 Z= 0.150 Angle : 0.541 7.190 15744 Z= 0.309 Chirality : 0.045 0.209 1772 Planarity : 0.002 0.019 1908 Dihedral : 14.632 138.007 1825 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.58 % Allowed : 20.16 % 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: -1.46 (0.23), residues: 1292 helix: 0.59 (0.32), residues: 252 sheet: -1.39 (0.23), residues: 476 loop : -1.17 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 313 TYR 0.019 0.001 TYR A 289 PHE 0.022 0.001 PHE A 258 HIS 0.005 0.001 HIS C 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (11579) covalent geometry : angle 0.54131 / 0.31 (15744) hydrogen bonds : bond 0.03419 / 2.17 ( 416) hydrogen bonds : angle 5.67748 / 3.88 ( 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 214 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 182 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7518 (pp30) REVERT: B 106 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7323 (pp30) REVERT: B 156 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8332 (mm) REVERT: C 72 TYR cc_start: 0.7717 (m-80) cc_final: 0.7480 (m-10) REVERT: C 106 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7425 (pp30) REVERT: C 342 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7343 (tm-30) REVERT: D 106 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7530 (pp30) REVERT: D 186 MET cc_start: 0.7723 (mtm) cc_final: 0.7390 (mtm) outliers start: 32 outliers final: 18 residues processed: 199 average time/residue: 0.0956 time to fit residues: 28.1235 Evaluate side-chains 194 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 106 GLN Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 185 MET 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 70 ASP Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 305 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 125 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.179678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.142762 restraints weight = 13092.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.142662 restraints weight = 12647.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.144347 restraints weight = 11684.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.144909 restraints weight = 9528.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.145788 restraints weight = 9173.659| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11579 Z= 0.193 Angle : 0.568 7.680 15744 Z= 0.322 Chirality : 0.045 0.203 1772 Planarity : 0.003 0.016 1908 Dihedral : 14.787 138.272 1825 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.06 % Allowed : 20.48 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.23), residues: 1292 helix: 0.63 (0.32), residues: 252 sheet: -1.58 (0.24), residues: 436 loop : -1.10 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 286 TYR 0.016 0.001 TYR A 289 PHE 0.017 0.001 PHE A 135 HIS 0.005 0.001 HIS D 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (11579) covalent geometry : angle 0.56778 / 0.32 (15744) hydrogen bonds : bond 0.03569 / 2.25 ( 416) hydrogen bonds : angle 5.71476 / 3.91 ( 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 206 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7525 (pp30) REVERT: B 81 LYS cc_start: 0.8183 (mtpp) cc_final: 0.7898 (tttp) REVERT: B 106 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7278 (pp30) REVERT: C 72 TYR cc_start: 0.7699 (m-80) cc_final: 0.7484 (m-10) REVERT: C 106 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7447 (pp30) REVERT: C 156 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8267 (mm) REVERT: D 106 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7519 (pp30) REVERT: D 186 MET cc_start: 0.7835 (mtm) cc_final: 0.7507 (mtm) outliers start: 38 outliers final: 24 residues processed: 191 average time/residue: 0.0989 time to fit residues: 27.5933 Evaluate side-chains 193 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 106 GLN 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 288 ILE Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 185 MET 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 D residue 62 THR Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 308 THR 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: 10.0000 chunk 4 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN A 79 ASN ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 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 = 0.3953 r_free = 0.3953 target = 0.175226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.139085 restraints weight = 13212.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.138524 restraints weight = 15265.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.140272 restraints weight = 14250.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.140957 restraints weight = 11061.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.141916 restraints weight = 10489.675| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 11579 Z= 0.332 Angle : 0.704 7.674 15744 Z= 0.389 Chirality : 0.049 0.178 1772 Planarity : 0.004 0.029 1908 Dihedral : 15.031 140.085 1825 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.31 % Allowed : 20.16 % Favored : 76.53 % 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: -1.77 (0.23), residues: 1292 helix: 0.40 (0.32), residues: 248 sheet: -1.65 (0.23), residues: 468 loop : -1.31 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 109 TYR 0.018 0.002 TYR A 289 PHE 0.040 0.002 PHE C 135 HIS 0.005 0.002 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00771 / 0.33 (11579) covalent geometry : angle 0.70404 / 0.39 (15744) hydrogen bonds : bond 0.04314 / 2.69 ( 416) hydrogen bonds : angle 6.12027 / 4.18 ( 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 208 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 167 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: C 72 TYR cc_start: 0.7743 (m-80) cc_final: 0.7507 (m-10) REVERT: C 106 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7609 (pp30) REVERT: C 156 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8258 (mm) REVERT: C 305 LYS cc_start: 0.7961 (mmtt) cc_final: 0.7577 (mppt) REVERT: D 106 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7984 (pt0) REVERT: D 186 MET cc_start: 0.7901 (mtm) cc_final: 0.7655 (mtm) outliers start: 41 outliers final: 25 residues processed: 190 average time/residue: 0.0966 time to fit residues: 26.8623 Evaluate side-chains 187 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 321 THR Chi-restraints excluded: chain A residue 339 SER 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 288 ILE Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 106 GLN 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 266 ILE Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 234 LYS 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 6 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 120 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN A 106 GLN B 106 GLN C 67 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.180922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.143984 restraints weight = 13077.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.143284 restraints weight = 12513.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.145263 restraints weight = 12556.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.145717 restraints weight = 10077.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.146128 restraints weight = 10559.624| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11579 Z= 0.150 Angle : 0.567 7.851 15744 Z= 0.320 Chirality : 0.045 0.198 1772 Planarity : 0.003 0.023 1908 Dihedral : 14.899 138.551 1825 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.02 % Allowed : 21.37 % Favored : 76.61 % 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: -1.41 (0.23), residues: 1292 helix: 0.74 (0.33), residues: 248 sheet: -1.41 (0.23), residues: 476 loop : -1.11 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 286 TYR 0.019 0.001 TYR A 289 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 0.00323 / 0.15 (11579) covalent geometry : angle 0.56740 / 0.32 (15744) hydrogen bonds : bond 0.03456 / 2.20 ( 416) hydrogen bonds : angle 5.76799 / 3.94 ( 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 193 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 72 TYR cc_start: 0.7685 (m-80) cc_final: 0.7447 (m-10) REVERT: C 106 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7484 (pp30) REVERT: D 106 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7528 (pp30) REVERT: D 186 MET cc_start: 0.7740 (mtm) cc_final: 0.7449 (mtm) outliers start: 25 outliers final: 21 residues processed: 184 average time/residue: 0.0957 time to fit residues: 25.8929 Evaluate side-chains 179 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 106 GLN Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 234 LYS Chi-restraints excluded: chain D residue 283 THR 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: 5.9990 chunk 33 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 84 optimal weight: 30.0000 chunk 120 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 62 optimal weight: 0.0970 chunk 108 optimal weight: 20.0000 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN ** C 361 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 = 0.4003 r_free = 0.4003 target = 0.180445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.142858 restraints weight = 13090.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.141931 restraints weight = 12160.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.144072 restraints weight = 11528.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.144781 restraints weight = 9101.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.145615 restraints weight = 8994.116| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 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 : 0.009 0.411 11579 Z= 0.447 Angle : 1.015 59.199 15744 Z= 0.642 Chirality : 0.053 0.729 1772 Planarity : 0.006 0.162 1908 Dihedral : 14.902 138.574 1825 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.34 % Allowed : 21.13 % Favored : 76.53 % Cbeta Deviations : 0.24 % 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: -1.41 (0.23), residues: 1292 helix: 0.77 (0.33), residues: 248 sheet: -1.42 (0.23), residues: 476 loop : -1.13 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 286 TYR 0.015 0.001 TYR A 289 PHE 0.017 0.001 PHE A 135 HIS 0.005 0.001 HIS B 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00924 / 0.45 (11579) covalent geometry : angle 1.01455 / 0.64 (15744) hydrogen bonds : bond 0.03456 / 2.20 ( 416) hydrogen bonds : angle 5.77046 / 3.95 ( 1188) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1629.35 seconds wall clock time: 29 minutes 16.66 seconds (1756.66 seconds total)