Starting phenix.real_space_refine on Tue Jun 10 01:50:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ypo_34010/06_2025/7ypo_34010.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ypo_34010/06_2025/7ypo_34010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ypo_34010/06_2025/7ypo_34010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ypo_34010/06_2025/7ypo_34010.map" model { file = "/net/cci-nas-00/data/ceres_data/7ypo_34010/06_2025/7ypo_34010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ypo_34010/06_2025/7ypo_34010.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.19, per 1000 atoms: 0.63 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: 2.78 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 3.80 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: 4.09 Time building geometry restraints manager: 3.22 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=" CZ ARG C 313 " pdb=" NH2 ARG C 313 " ideal model delta sigma weight residual 1.330 1.317 0.013 1.30e-02 5.92e+03 1.03e+00 bond pdb=" CZ ARG D 313 " pdb=" NH2 ARG D 313 " ideal model delta sigma weight residual 1.330 1.317 0.013 1.30e-02 5.92e+03 1.03e+00 bond pdb=" CZ ARG B 313 " pdb=" NH2 ARG B 313 " ideal model delta sigma weight residual 1.330 1.317 0.013 1.30e-02 5.92e+03 1.01e+00 bond pdb=" C4' DA Q 26 " pdb=" O4' DA Q 26 " ideal model delta sigma weight residual 1.450 1.430 0.020 2.00e-02 2.50e+03 9.93e-01 bond pdb=" CZ ARG A 313 " pdb=" NH2 ARG A 313 " ideal model delta sigma weight residual 1.330 1.318 0.012 1.30e-02 5.92e+03 9.02e-01 ... (remaining 11574 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 14956 1.21 - 2.42: 668 2.42 - 3.63: 100 3.63 - 4.83: 16 4.83 - 6.04: 4 Bond angle restraints: 15744 Sorted by residual: 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 angle pdb=" C ARG C 109 " pdb=" N LYS C 110 " pdb=" CA LYS C 110 " ideal model delta sigma weight residual 121.54 127.55 -6.01 1.91e+00 2.74e-01 9.89e+00 angle pdb=" C ILE B 66 " pdb=" N ASN B 67 " pdb=" CA ASN B 67 " ideal model delta sigma weight residual 122.82 126.13 -3.31 1.42e+00 4.96e-01 5.42e+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: 1053 0.029 - 0.059: 426 0.059 - 0.088: 167 0.088 - 0.117: 99 0.117 - 0.147: 27 Chirality restraints: 1772 Sorted by residual: chirality pdb=" CA ILE B 83 " pdb=" N ILE B 83 " pdb=" C ILE B 83 " pdb=" CB ILE B 83 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.38e-01 chirality pdb=" CA ILE A 83 " pdb=" N ILE A 83 " pdb=" C ILE A 83 " pdb=" CB ILE A 83 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA ILE D 83 " pdb=" N ILE D 83 " pdb=" C ILE D 83 " pdb=" CB ILE D 83 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.25e-01 ... (remaining 1769 not shown) Planarity restraints: 1908 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 152 " -0.007 2.00e-02 2.50e+03 6.35e-03 8.06e-01 pdb=" CG TYR B 152 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR B 152 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 152 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 152 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 152 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 152 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 152 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 152 " -0.007 2.00e-02 2.50e+03 6.15e-03 7.58e-01 pdb=" CG TYR A 152 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR A 152 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 152 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 152 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 152 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 152 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 152 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 152 " 0.007 2.00e-02 2.50e+03 6.09e-03 7.42e-01 pdb=" CG TYR D 152 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR D 152 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR D 152 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR D 152 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR D 152 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 152 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 152 " 0.001 2.00e-02 2.50e+03 ... (remaining 1905 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 172 2.65 - 3.21: 10736 3.21 - 3.78: 16580 3.78 - 4.34: 23545 4.34 - 4.90: 38894 Nonbonded interactions: 89927 Sorted by model distance: nonbonded pdb=" OD1 ASP D 188 " pdb=" N PHE D 189 " model vdw 2.091 3.120 nonbonded pdb=" OD1 ASP C 188 " pdb=" N PHE C 189 " model vdw 2.091 3.120 nonbonded pdb=" OD1 ASP B 188 " pdb=" N PHE B 189 " model vdw 2.091 3.120 nonbonded pdb=" OD1 ASP A 188 " pdb=" N PHE A 189 " model vdw 2.091 3.120 nonbonded pdb=" NE2 GLN A 119 " pdb=" O CYS A 120 " model vdw 2.241 3.120 ... (remaining 89922 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 31.510 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 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 0.025 11579 Z= 0.172 Angle : 0.586 6.042 15744 Z= 0.343 Chirality : 0.044 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 : 11.72 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.007 0.002 HIS A 228 PHE 0.014 0.001 PHE A 295 TYR 0.016 0.001 TYR B 152 ARG 0.003 0.001 ARG B 223 Details of bonding type rmsd hydrogen bonds : bond 0.11464 ( 416) hydrogen bonds : angle 7.40723 ( 1188) covalent geometry : bond 0.00379 (11579) covalent geometry : angle 0.58634 (15744) *********************** 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 : 1.294 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: 0.1852 time to fit residues: 67.7046 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 : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 118 optimal weight: 6.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 119 GLN B 68 ASN B 119 GLN B 229 ASN C 68 ASN C 91 GLN C 119 GLN C 232 ASN C 270 ASN D 68 ASN ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 GLN D 232 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.176785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.140644 restraints weight = 13157.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.140371 restraints weight = 14142.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.141987 restraints weight = 13653.653| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 11579 Z= 0.252 Angle : 0.644 5.432 15744 Z= 0.365 Chirality : 0.047 0.175 1772 Planarity : 0.003 0.037 1908 Dihedral : 14.555 140.081 1825 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.85 % Allowed : 11.94 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.23), residues: 1292 helix: 0.37 (0.32), residues: 248 sheet: -1.67 (0.22), residues: 484 loop : -1.25 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 228 PHE 0.022 0.002 PHE A 135 TYR 0.023 0.002 TYR D 299 ARG 0.004 0.001 ARG B 286 Details of bonding type rmsd hydrogen bonds : bond 0.04120 ( 416) hydrogen bonds : angle 6.28020 ( 1188) covalent geometry : bond 0.00591 (11579) covalent geometry : angle 0.64436 (15744) *********************** 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 214 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 191 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 ARG cc_start: 0.7290 (mtt90) cc_final: 0.7026 (mtt-85) REVERT: C 55 LYS cc_start: 0.8759 (ttmt) cc_final: 0.8485 (tttt) REVERT: C 190 LYS cc_start: 0.8036 (ptpp) cc_final: 0.7760 (ptpp) REVERT: C 349 ASP cc_start: 0.7484 (m-30) cc_final: 0.7229 (m-30) REVERT: D 68 ASN cc_start: 0.7105 (m110) cc_final: 0.6882 (m110) REVERT: D 186 MET cc_start: 0.7891 (mtm) cc_final: 0.7643 (mtm) outliers start: 23 outliers final: 16 residues processed: 206 average time/residue: 0.2178 time to fit residues: 66.1631 Evaluate side-chains 183 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 228 HIS 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 339 SER Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 339 SER 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 37 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 19 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 ASN C 232 ASN ** C 361 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 = 0.3988 r_free = 0.3988 target = 0.178584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.142923 restraints weight = 13281.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.142632 restraints weight = 14205.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.144319 restraints weight = 13453.469| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 11579 Z= 0.195 Angle : 0.568 5.974 15744 Z= 0.324 Chirality : 0.045 0.159 1772 Planarity : 0.003 0.022 1908 Dihedral : 15.235 138.642 1825 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.42 % Allowed : 15.89 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.23), residues: 1292 helix: 0.58 (0.32), residues: 248 sheet: -1.53 (0.23), residues: 464 loop : -1.17 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 228 PHE 0.021 0.002 PHE A 135 TYR 0.013 0.001 TYR D 299 ARG 0.003 0.000 ARG B 286 Details of bonding type rmsd hydrogen bonds : bond 0.03650 ( 416) hydrogen bonds : angle 5.90023 ( 1188) covalent geometry : bond 0.00455 (11579) covalent geometry : angle 0.56831 (15744) *********************** 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 223 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLN cc_start: 0.7768 (tt0) cc_final: 0.7542 (tt0) REVERT: C 156 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8164 (mm) REVERT: C 273 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7993 (mt) REVERT: C 349 ASP cc_start: 0.7355 (m-30) cc_final: 0.7097 (m-30) REVERT: D 186 MET cc_start: 0.7835 (mtm) cc_final: 0.7566 (mtm) outliers start: 30 outliers final: 20 residues processed: 211 average time/residue: 0.2150 time to fit residues: 66.6095 Evaluate side-chains 192 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET 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 156 ILE Chi-restraints excluded: chain B residue 160 SER 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 339 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 321 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 200 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 0 optimal weight: 30.0000 chunk 7 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 108 optimal weight: 0.0060 chunk 58 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 59 optimal weight: 0.6980 chunk 113 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 overall best weight: 2.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.173446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.134234 restraints weight = 13370.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.133633 restraints weight = 13679.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.135418 restraints weight = 12877.651| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 11579 Z= 0.220 Angle : 0.588 6.374 15744 Z= 0.332 Chirality : 0.045 0.165 1772 Planarity : 0.003 0.022 1908 Dihedral : 15.237 138.867 1825 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.15 % Allowed : 17.90 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.23), residues: 1292 helix: 0.47 (0.31), residues: 248 sheet: -1.56 (0.24), residues: 464 loop : -1.14 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 228 PHE 0.022 0.002 PHE A 135 TYR 0.014 0.001 TYR D 299 ARG 0.004 0.001 ARG B 313 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 416) hydrogen bonds : angle 5.87514 ( 1188) covalent geometry : bond 0.00514 (11579) covalent geometry : angle 0.58755 (15744) *********************** 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 229 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 190 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLN cc_start: 0.7690 (mm-40) cc_final: 0.7432 (mp10) REVERT: A 209 ASP cc_start: 0.7640 (t0) cc_final: 0.7385 (t0) REVERT: B 69 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6965 (tt0) REVERT: C 156 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8190 (mm) REVERT: C 232 ASN cc_start: 0.7912 (t0) cc_final: 0.7665 (p0) REVERT: C 342 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7421 (tm-30) REVERT: C 349 ASP cc_start: 0.7471 (m-30) cc_final: 0.7182 (m-30) REVERT: D 106 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7458 (pp30) REVERT: D 186 MET cc_start: 0.7954 (mtm) cc_final: 0.7634 (mtm) outliers start: 39 outliers final: 22 residues processed: 215 average time/residue: 0.2172 time to fit residues: 69.2333 Evaluate side-chains 189 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET 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 B residue 69 GLU Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 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 B residue 308 THR Chi-restraints excluded: chain B residue 339 SER 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 253 MET Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 339 SER 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 88 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 126 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 67 ASN A 106 GLN ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.174666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.135650 restraints weight = 13127.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.134961 restraints weight = 11905.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.136850 restraints weight = 11645.724| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11579 Z= 0.163 Angle : 0.530 6.098 15744 Z= 0.303 Chirality : 0.044 0.153 1772 Planarity : 0.002 0.018 1908 Dihedral : 15.152 137.957 1825 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.50 % Allowed : 19.44 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.23), residues: 1292 helix: 0.81 (0.32), residues: 248 sheet: -1.45 (0.23), residues: 480 loop : -0.98 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 228 PHE 0.020 0.001 PHE A 258 TYR 0.012 0.001 TYR D 299 ARG 0.003 0.000 ARG B 286 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 416) hydrogen bonds : angle 5.58269 ( 1188) covalent geometry : bond 0.00374 (11579) covalent geometry : angle 0.53003 (15744) *********************** 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 229 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 LYS cc_start: 0.8197 (tttp) cc_final: 0.7913 (tttp) REVERT: C 232 ASN cc_start: 0.7842 (t0) cc_final: 0.7604 (p0) REVERT: C 342 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7415 (tm-30) REVERT: C 349 ASP cc_start: 0.7473 (m-30) cc_final: 0.7159 (m-30) REVERT: D 186 MET cc_start: 0.7850 (mtm) cc_final: 0.7554 (mtm) outliers start: 31 outliers final: 20 residues processed: 218 average time/residue: 0.2193 time to fit residues: 69.4584 Evaluate side-chains 189 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET 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 288 ILE 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 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 253 MET Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 308 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 76 optimal weight: 9.9990 chunk 118 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 30 optimal weight: 0.0980 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 106 GLN B 106 GLN ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.173439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.134795 restraints weight = 13433.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.134230 restraints weight = 13192.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.135830 restraints weight = 12325.885| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11579 Z= 0.193 Angle : 0.563 7.291 15744 Z= 0.318 Chirality : 0.044 0.173 1772 Planarity : 0.003 0.018 1908 Dihedral : 15.197 138.928 1825 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.31 % Allowed : 19.03 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.23), residues: 1292 helix: 0.87 (0.32), residues: 248 sheet: -1.60 (0.24), residues: 436 loop : -1.04 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 228 PHE 0.029 0.002 PHE C 135 TYR 0.015 0.001 TYR D 299 ARG 0.003 0.000 ARG A 286 Details of bonding type rmsd hydrogen bonds : bond 0.03581 ( 416) hydrogen bonds : angle 5.64364 ( 1188) covalent geometry : bond 0.00449 (11579) covalent geometry : angle 0.56287 (15744) *********************** 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 229 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 188 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 TYR cc_start: 0.8255 (m-80) cc_final: 0.8022 (m-10) REVERT: B 377 GLU cc_start: 0.8186 (tp30) cc_final: 0.7833 (tp30) REVERT: C 156 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8190 (mm) REVERT: C 232 ASN cc_start: 0.7879 (t0) cc_final: 0.7597 (p0) REVERT: C 246 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.7282 (mtm-85) REVERT: C 342 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7445 (tm-30) REVERT: C 349 ASP cc_start: 0.7460 (m-30) cc_final: 0.7134 (m-30) REVERT: D 106 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7433 (pp30) REVERT: D 186 MET cc_start: 0.7831 (mtm) cc_final: 0.7551 (mtm) outliers start: 41 outliers final: 28 residues processed: 215 average time/residue: 0.2159 time to fit residues: 67.6122 Evaluate side-chains 201 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET 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 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 279 THR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 246 ARG 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 C residue 321 THR Chi-restraints excluded: chain C residue 339 SER 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 308 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 90 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 71 optimal weight: 0.0970 chunk 126 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 316 ASN B 106 GLN ** C 361 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 = 0.3945 r_free = 0.3945 target = 0.174817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.135733 restraints weight = 13470.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.135301 restraints weight = 13934.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.137036 restraints weight = 12816.225| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11579 Z= 0.192 Angle : 0.561 6.947 15744 Z= 0.316 Chirality : 0.044 0.160 1772 Planarity : 0.003 0.018 1908 Dihedral : 15.253 139.352 1825 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.47 % Allowed : 19.35 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.23), residues: 1292 helix: 0.80 (0.32), residues: 248 sheet: -1.58 (0.24), residues: 436 loop : -1.01 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 228 PHE 0.021 0.002 PHE A 135 TYR 0.013 0.001 TYR D 299 ARG 0.003 0.000 ARG A 286 Details of bonding type rmsd hydrogen bonds : bond 0.03589 ( 416) hydrogen bonds : angle 5.67088 ( 1188) covalent geometry : bond 0.00447 (11579) covalent geometry : angle 0.56131 (15744) *********************** 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 219 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 176 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 TYR cc_start: 0.8303 (m-80) cc_final: 0.8080 (m-10) REVERT: B 69 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6900 (tt0) REVERT: C 156 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8186 (mm) REVERT: C 232 ASN cc_start: 0.7904 (t0) cc_final: 0.7523 (p0) REVERT: C 246 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.7260 (mtm-85) REVERT: C 349 ASP cc_start: 0.7471 (m-30) cc_final: 0.7142 (m-30) REVERT: D 106 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7960 (pt0) REVERT: D 186 MET cc_start: 0.7933 (mtm) cc_final: 0.7682 (mtm) outliers start: 43 outliers final: 34 residues processed: 205 average time/residue: 0.2094 time to fit residues: 63.0540 Evaluate side-chains 197 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET 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 308 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 69 GLU 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 185 MET Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 364 ILE 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 308 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 0 optimal weight: 30.0000 chunk 1 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 39 optimal weight: 0.3980 chunk 47 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 79 ASN A 106 GLN B 106 GLN ** C 361 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 = 0.3942 r_free = 0.3942 target = 0.174237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.135377 restraints weight = 13469.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.134606 restraints weight = 13183.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.136465 restraints weight = 12304.087| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11579 Z= 0.175 Angle : 0.555 7.070 15744 Z= 0.313 Chirality : 0.044 0.158 1772 Planarity : 0.003 0.023 1908 Dihedral : 15.275 139.335 1825 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.39 % Allowed : 19.60 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.23), residues: 1292 helix: 0.90 (0.32), residues: 248 sheet: -1.36 (0.23), residues: 476 loop : -0.99 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 228 PHE 0.033 0.002 PHE C 135 TYR 0.014 0.001 TYR A 107 ARG 0.003 0.000 ARG A 286 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 416) hydrogen bonds : angle 5.60572 ( 1188) covalent geometry : bond 0.00404 (11579) covalent geometry : angle 0.55453 (15744) *********************** 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 219 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 TYR cc_start: 0.8284 (m-80) cc_final: 0.8051 (m-10) REVERT: B 69 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6969 (tt0) REVERT: B 377 GLU cc_start: 0.8275 (tp30) cc_final: 0.7695 (tp30) REVERT: C 156 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8174 (mm) REVERT: C 232 ASN cc_start: 0.7863 (t0) cc_final: 0.7503 (p0) REVERT: C 246 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.7249 (mtm-85) REVERT: C 342 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7426 (tm-30) REVERT: C 349 ASP cc_start: 0.7398 (m-30) cc_final: 0.7084 (m-30) REVERT: D 106 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7943 (pt0) REVERT: D 186 MET cc_start: 0.7836 (mtm) cc_final: 0.7573 (mtm) REVERT: D 246 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7108 (mtm-85) outliers start: 42 outliers final: 30 residues processed: 205 average time/residue: 0.2219 time to fit residues: 65.8804 Evaluate side-chains 199 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET 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 69 GLU 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 279 THR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 364 ILE 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 246 ARG 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 7 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 8 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 106 GLN B 106 GLN ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.176016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.137589 restraints weight = 13351.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.137874 restraints weight = 12547.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.139376 restraints weight = 11852.558| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3048 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= 0.146 Angle : 0.537 7.294 15744 Z= 0.304 Chirality : 0.044 0.157 1772 Planarity : 0.002 0.023 1908 Dihedral : 15.280 138.893 1825 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.82 % Allowed : 20.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.23), residues: 1292 helix: 0.93 (0.32), residues: 252 sheet: -1.26 (0.23), residues: 476 loop : -1.00 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 228 PHE 0.019 0.001 PHE A 135 TYR 0.014 0.001 TYR A 107 ARG 0.005 0.001 ARG B 313 Details of bonding type rmsd hydrogen bonds : bond 0.03326 ( 416) hydrogen bonds : angle 5.47978 ( 1188) covalent geometry : bond 0.00331 (11579) covalent geometry : angle 0.53651 (15744) *********************** 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 220 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 TYR cc_start: 0.8289 (m-80) cc_final: 0.8064 (m-10) REVERT: B 377 GLU cc_start: 0.8233 (tp30) cc_final: 0.7722 (tp30) REVERT: C 232 ASN cc_start: 0.7843 (t0) cc_final: 0.7428 (p0) REVERT: C 342 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7407 (tm-30) REVERT: C 349 ASP cc_start: 0.7486 (m-30) cc_final: 0.7180 (m-30) REVERT: D 106 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7880 (pt0) REVERT: D 186 MET cc_start: 0.7734 (mtm) cc_final: 0.7506 (mtm) REVERT: D 246 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7099 (mtm-85) outliers start: 35 outliers final: 24 residues processed: 205 average time/residue: 0.3021 time to fit residues: 90.6433 Evaluate side-chains 196 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET 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 127 MET Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 70 ASP Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 339 SER 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 246 ARG 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 76 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 chunk 118 optimal weight: 0.0170 chunk 28 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 12 optimal weight: 0.2980 chunk 89 optimal weight: 0.9990 overall best weight: 0.6622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 106 GLN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 ASN ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.179332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.141433 restraints weight = 13184.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.141119 restraints weight = 11855.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.143161 restraints weight = 11968.581| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11579 Z= 0.114 Angle : 0.520 9.555 15744 Z= 0.291 Chirality : 0.043 0.158 1772 Planarity : 0.002 0.017 1908 Dihedral : 15.167 137.547 1825 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.77 % Allowed : 21.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.23), residues: 1292 helix: 1.06 (0.32), residues: 252 sheet: -1.11 (0.23), residues: 476 loop : -0.86 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 228 PHE 0.032 0.001 PHE C 135 TYR 0.030 0.001 TYR A 107 ARG 0.006 0.001 ARG A 109 Details of bonding type rmsd hydrogen bonds : bond 0.03119 ( 416) hydrogen bonds : angle 5.21602 ( 1188) covalent geometry : bond 0.00247 (11579) covalent geometry : angle 0.52005 (15744) ********************** 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 231 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 209 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.7346 (t0) cc_final: 0.7074 (t0) REVERT: A 231 ASN cc_start: 0.8367 (t0) cc_final: 0.8128 (t0) REVERT: C 117 TYR cc_start: 0.8247 (p90) cc_final: 0.8017 (p90) REVERT: C 232 ASN cc_start: 0.7830 (t0) cc_final: 0.7396 (p0) REVERT: D 106 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7226 (pp30) outliers start: 22 outliers final: 14 residues processed: 223 average time/residue: 0.2681 time to fit residues: 89.2982 Evaluate side-chains 190 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 361 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 122 optimal weight: 0.0770 chunk 41 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 106 GLN B 79 ASN ** B 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.173419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.134580 restraints weight = 13380.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.133848 restraints weight = 14235.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.135614 restraints weight = 12981.706| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 11579 Z= 0.243 Angle : 0.628 7.902 15744 Z= 0.349 Chirality : 0.046 0.155 1772 Planarity : 0.003 0.029 1908 Dihedral : 15.311 140.362 1825 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.02 % Allowed : 22.58 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.23), residues: 1292 helix: 0.75 (0.31), residues: 248 sheet: -1.23 (0.23), residues: 468 loop : -1.00 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 228 PHE 0.027 0.002 PHE B 295 TYR 0.018 0.002 TYR B 157 ARG 0.005 0.001 ARG A 268 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 416) hydrogen bonds : angle 5.70451 ( 1188) covalent geometry : bond 0.00571 (11579) covalent geometry : angle 0.62796 (15744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3837.47 seconds wall clock time: 69 minutes 54.12 seconds (4194.12 seconds total)