Starting phenix.real_space_refine on Wed May 14 01:01:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ypo_34010/05_2025/7ypo_34010.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ypo_34010/05_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_34010/05_2025/7ypo_34010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ypo_34010/05_2025/7ypo_34010.map" model { file = "/net/cci-nas-00/data/ceres_data/7ypo_34010/05_2025/7ypo_34010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ypo_34010/05_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-5687/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: 6.56, per 1000 atoms: 0.58 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: 2.48 Conformation dependent library (CDL) restraints added in 1.4 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: 3.91 Creating SS restraints... Processing helix chain 'A' and resid 88 through 95 Processing helix chain 'A' and resid 135 through 141 Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 203 through 213 Processing helix chain 'A' and resid 319 through 343 removed outlier: 3.543A pdb=" N ASP A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 95 Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'B' and resid 188 through 196 Processing helix chain 'B' and resid 203 through 213 Processing helix chain 'B' and resid 319 through 343 removed outlier: 3.542A pdb=" N ASP B 324 " --> pdb=" O LYS B 320 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN B 338 " --> pdb=" O LEU B 334 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 95 Processing helix chain 'C' and resid 135 through 141 Processing helix chain 'C' and resid 188 through 196 Processing helix chain 'C' and resid 203 through 213 Processing helix chain 'C' and resid 319 through 343 removed outlier: 3.542A pdb=" N ASP C 324 " --> pdb=" O LYS C 320 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN C 338 " --> pdb=" O LEU C 334 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER C 339 " --> pdb=" O SER C 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 95 Processing helix chain 'D' and resid 135 through 141 Processing helix chain 'D' and resid 188 through 196 Processing helix chain 'D' and resid 203 through 213 Processing helix chain 'D' and resid 319 through 343 removed outlier: 3.542A pdb=" N ASP D 324 " --> pdb=" O LYS D 320 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN D 338 " --> pdb=" O LEU D 334 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER D 339 " --> pdb=" O SER D 335 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 87 removed outlier: 4.247A pdb=" N TYR A 72 " --> pdb=" O GLY A 87 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLU A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER A 65 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TYR A 71 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR A 63 " --> pdb=" O TYR A 71 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU A 73 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LYS A 61 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LYS A 75 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLU A 102 " --> pdb=" O TYR A 117 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TYR A 117 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL A 104 " --> pdb=" O LYS A 115 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 134 removed outlier: 6.392A pdb=" N VAL A 133 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 133 through 134 removed outlier: 6.392A pdb=" N VAL A 133 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LYS A 164 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLY A 153 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL A 166 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU A 170 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N LEU A 147 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 11.540A pdb=" N GLU A 172 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 14.796A pdb=" N SER A 145 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LYS A 144 " --> pdb=" O ARG A 223 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE A 224 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 10.189A pdb=" N ASN A 241 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 228 Processing sheet with id=AA5, first strand: chain 'A' and resid 272 through 277 removed outlier: 5.717A pdb=" N VAL A 353 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE A 364 " --> pdb=" O VAL A 353 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 282 through 288 Processing sheet with id=AA7, first strand: chain 'B' and resid 81 through 87 removed outlier: 4.247A pdb=" N TYR B 72 " --> pdb=" O GLY B 87 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLU B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER B 65 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TYR B 71 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR B 63 " --> pdb=" O TYR B 71 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU B 73 " --> pdb=" O LYS B 61 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS B 61 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LYS B 75 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLU B 102 " --> pdb=" O TYR B 117 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR B 117 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL B 104 " --> pdb=" O LYS B 115 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 133 through 134 removed outlier: 6.392A pdb=" N VAL B 133 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 133 through 134 removed outlier: 6.392A pdb=" N VAL B 133 " --> pdb=" O GLU B 172 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LYS B 164 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLY B 153 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL B 166 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU B 170 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N LEU B 147 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 11.540A pdb=" N GLU B 172 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 14.796A pdb=" N SER B 145 " --> pdb=" O GLU B 172 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LYS B 144 " --> pdb=" O ARG B 223 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE B 224 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N ASN B 241 " --> pdb=" O ILE B 224 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 227 through 228 Processing sheet with id=AB2, first strand: chain 'B' and resid 272 through 277 removed outlier: 5.716A pdb=" N VAL B 353 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE B 364 " --> pdb=" O VAL B 353 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 282 through 288 Processing sheet with id=AB4, first strand: chain 'C' and resid 81 through 87 removed outlier: 4.246A pdb=" N TYR C 72 " --> pdb=" O GLY C 87 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLU C 69 " --> pdb=" O SER C 65 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER C 65 " --> pdb=" O GLU C 69 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TYR C 71 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR C 63 " --> pdb=" O TYR C 71 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU C 73 " --> pdb=" O LYS C 61 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS C 61 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LYS C 75 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLU C 102 " --> pdb=" O TYR C 117 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TYR C 117 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL C 104 " --> pdb=" O LYS C 115 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 133 through 134 removed outlier: 6.392A pdb=" N VAL C 133 " --> pdb=" O GLU C 172 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 133 through 134 removed outlier: 6.392A pdb=" N VAL C 133 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LYS C 164 " --> pdb=" O GLY C 153 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLY C 153 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL C 166 " --> pdb=" O LEU C 151 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU C 170 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N LEU C 147 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 11.540A pdb=" N GLU C 172 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 14.796A pdb=" N SER C 145 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LYS C 144 " --> pdb=" O ARG C 223 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE C 224 " --> pdb=" O ASN C 241 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N ASN C 241 " --> pdb=" O ILE C 224 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 227 through 228 Processing sheet with id=AB8, first strand: chain 'C' and resid 272 through 277 removed outlier: 5.716A pdb=" N VAL C 353 " --> pdb=" O ILE C 364 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE C 364 " --> pdb=" O VAL C 353 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 282 through 288 Processing sheet with id=AC1, first strand: chain 'D' and resid 81 through 87 removed outlier: 4.246A pdb=" N TYR D 72 " --> pdb=" O GLY D 87 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLU D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER D 65 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TYR D 71 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR D 63 " --> pdb=" O TYR D 71 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU D 73 " --> pdb=" O LYS D 61 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS D 61 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LYS D 75 " --> pdb=" O LEU D 59 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLU D 102 " --> pdb=" O TYR D 117 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TYR D 117 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL D 104 " --> pdb=" O LYS D 115 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 133 through 134 removed outlier: 6.392A pdb=" N VAL D 133 " --> pdb=" O GLU D 172 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 133 through 134 removed outlier: 6.392A pdb=" N VAL D 133 " --> pdb=" O GLU D 172 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LYS D 164 " --> pdb=" O GLY D 153 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLY D 153 " --> pdb=" O LYS D 164 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL D 166 " --> pdb=" O LEU D 151 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU D 170 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N LEU D 147 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 11.540A pdb=" N GLU D 172 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 14.796A pdb=" N SER D 145 " --> pdb=" O GLU D 172 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N LYS D 144 " --> pdb=" O ARG D 223 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE D 224 " --> pdb=" O ASN D 241 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N ASN D 241 " --> pdb=" O ILE D 224 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 227 through 228 Processing sheet with id=AC5, first strand: chain 'D' and resid 272 through 277 removed outlier: 5.717A pdb=" N VAL D 353 " --> pdb=" O ILE D 364 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE D 364 " --> pdb=" O VAL D 353 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 282 through 288 416 hydrogen bonds defined for protein. 1188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 3.91 Time building geometry restraints manager: 2.93 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: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.640 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.770 ------------------------------------------------------------------------------- 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 : 1.187 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: 0.1764 time to fit residues: 64.5090 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 : 1.160 ------------------------------------------------------------------------------- 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 = 0.3598 r_free = 0.3598 target = 0.140616 restraints weight = 13157.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.140319 restraints weight = 14139.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.141945 restraints weight = 13661.557| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 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 : 1.265 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: 0.8486 (tttt) REVERT: C 190 LYS cc_start: 0.8035 (ptpp) cc_final: 0.7760 (ptpp) REVERT: C 349 ASP cc_start: 0.7486 (m-30) cc_final: 0.7230 (m-30) REVERT: D 68 ASN cc_start: 0.7107 (m110) cc_final: 0.6883 (m110) REVERT: D 186 MET cc_start: 0.7892 (mtm) cc_final: 0.7642 (mtm) outliers start: 23 outliers final: 16 residues processed: 206 average time/residue: 0.2005 time to fit residues: 61.2495 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 : 1.231 ------------------------------------------------------------------------------- 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: 9.9990 chunk 86 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN B 229 ASN C 232 ASN ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.179292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.142626 restraints weight = 13244.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.142129 restraints weight = 13440.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.143956 restraints weight = 12841.473| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2089 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= 0.178 Angle : 0.557 6.087 15744 Z= 0.318 Chirality : 0.044 0.157 1772 Planarity : 0.003 0.023 1908 Dihedral : 15.127 138.383 1825 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.94 % Allowed : 15.81 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.51 (0.23), residues: 1292 helix: 0.61 (0.32), residues: 248 sheet: -1.53 (0.23), residues: 480 loop : -1.09 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 228 PHE 0.021 0.001 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 0.03579 ( 416) hydrogen bonds : angle 5.86605 ( 1188) covalent geometry : bond 0.00413 (11579) covalent geometry : angle 0.55689 (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 214 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.6925 (tptt) cc_final: 0.6272 (tptp) REVERT: B 313 ARG cc_start: 0.7142 (mtt90) cc_final: 0.6891 (mtm-85) REVERT: C 55 LYS cc_start: 0.8768 (ttmt) cc_final: 0.8473 (tttt) REVERT: C 156 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.8198 (mm) REVERT: C 349 ASP cc_start: 0.7361 (m-30) cc_final: 0.7088 (m-30) REVERT: D 186 MET cc_start: 0.7843 (mtm) cc_final: 0.7577 (mtm) outliers start: 24 outliers final: 16 residues processed: 202 average time/residue: 0.2118 time to fit residues: 62.7042 Evaluate side-chains 187 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 1.356 ------------------------------------------------------------------------------- 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 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 288 ILE Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 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: 20.0000 chunk 9 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 108 optimal weight: 20.0000 chunk 58 optimal weight: 7.9990 chunk 21 optimal weight: 0.5980 chunk 1 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 113 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.177451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.140303 restraints weight = 13183.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.140124 restraints weight = 13645.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.141746 restraints weight = 13070.219| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 11579 Z= 0.205 Angle : 0.572 6.400 15744 Z= 0.324 Chirality : 0.044 0.163 1772 Planarity : 0.003 0.021 1908 Dihedral : 15.232 138.562 1825 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.06 % Allowed : 17.42 % Favored : 79.52 % 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: -1.53 (0.23), residues: 1292 helix: 0.51 (0.31), residues: 248 sheet: -1.52 (0.24), residues: 464 loop : -1.10 (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 0.003 0.000 ARG A 286 Details of bonding type rmsd hydrogen bonds : bond 0.03679 ( 416) hydrogen bonds : angle 5.80635 ( 1188) covalent geometry : bond 0.00476 (11579) covalent geometry : angle 0.57175 (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 234 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 196 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.7506 (t0) cc_final: 0.7268 (t0) REVERT: C 106 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7467 (pp30) REVERT: C 156 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8225 (mm) REVERT: C 232 ASN cc_start: 0.7780 (t0) cc_final: 0.7535 (p0) REVERT: C 349 ASP cc_start: 0.7399 (m-30) cc_final: 0.7124 (m-30) REVERT: D 186 MET cc_start: 0.7867 (mtm) cc_final: 0.7538 (mtm) outliers start: 38 outliers final: 26 residues processed: 220 average time/residue: 0.2099 time to fit residues: 67.9977 Evaluate side-chains 195 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 1.281 ------------------------------------------------------------------------------- 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 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 106 GLN Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain 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 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: 3.9990 chunk 41 optimal weight: 6.9990 chunk 126 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 316 ASN ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.173290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.134258 restraints weight = 13202.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.133771 restraints weight = 13111.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.135459 restraints weight = 12488.089| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11579 Z= 0.153 Angle : 0.526 6.278 15744 Z= 0.301 Chirality : 0.044 0.153 1772 Planarity : 0.002 0.017 1908 Dihedral : 15.133 137.646 1825 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.50 % Allowed : 18.87 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.31 (0.23), residues: 1292 helix: 0.73 (0.31), residues: 248 sheet: -1.41 (0.23), residues: 480 loop : -0.92 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 228 PHE 0.020 0.001 PHE A 258 TYR 0.014 0.001 TYR D 299 ARG 0.006 0.000 ARG B 313 Details of bonding type rmsd hydrogen bonds : bond 0.03355 ( 416) hydrogen bonds : angle 5.54664 ( 1188) covalent geometry : bond 0.00349 (11579) covalent geometry : angle 0.52626 (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 228 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 197 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6787 (tt0) REVERT: B 106 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7336 (pp30) REVERT: C 55 LYS cc_start: 0.8746 (ttmt) cc_final: 0.8514 (ttmt) REVERT: C 68 ASN cc_start: 0.8548 (m-40) cc_final: 0.8340 (m-40) REVERT: C 72 TYR cc_start: 0.7736 (m-10) cc_final: 0.7478 (m-10) REVERT: C 232 ASN cc_start: 0.7828 (t0) cc_final: 0.7505 (p0) REVERT: C 349 ASP cc_start: 0.7430 (m-30) cc_final: 0.7125 (m-30) REVERT: D 106 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7446 (pp30) REVERT: D 186 MET cc_start: 0.7941 (mtm) cc_final: 0.7614 (mtm) outliers start: 31 outliers final: 19 residues processed: 214 average time/residue: 0.2105 time to fit residues: 65.4731 Evaluate side-chains 199 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 106 GLN Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain 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 90 THR Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain 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 106 GLN Chi-restraints excluded: chain D residue 200 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 76 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 chunk 105 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 30 optimal weight: 0.0770 overall best weight: 3.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 316 ASN ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.172419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.133266 restraints weight = 13479.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.132131 restraints weight = 13884.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.133990 restraints weight = 12995.157| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 11579 Z= 0.238 Angle : 0.598 7.254 15744 Z= 0.336 Chirality : 0.045 0.165 1772 Planarity : 0.003 0.022 1908 Dihedral : 15.200 139.932 1825 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.39 % Allowed : 18.95 % 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: -1.44 (0.23), residues: 1292 helix: 0.60 (0.31), residues: 248 sheet: -1.47 (0.24), residues: 464 loop : -1.05 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 228 PHE 0.025 0.002 PHE B 295 TYR 0.014 0.001 TYR B 289 ARG 0.004 0.001 ARG A 286 Details of bonding type rmsd hydrogen bonds : bond 0.03848 ( 416) hydrogen bonds : angle 5.83544 ( 1188) covalent geometry : bond 0.00557 (11579) covalent geometry : angle 0.59792 (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 217 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 175 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6905 (tt0) REVERT: C 156 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8199 (mm) REVERT: C 232 ASN cc_start: 0.7875 (t0) cc_final: 0.7581 (p0) REVERT: C 349 ASP cc_start: 0.7485 (m-30) cc_final: 0.7184 (m-30) REVERT: D 106 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7978 (pp30) REVERT: D 186 MET cc_start: 0.7978 (mtm) cc_final: 0.7700 (mtm) outliers start: 42 outliers final: 27 residues processed: 202 average time/residue: 0.2174 time to fit residues: 65.2671 Evaluate side-chains 188 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 1.289 ------------------------------------------------------------------------------- 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 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 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 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: 9.9990 chunk 51 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 2 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 316 ASN B 106 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3876 r_free = 0.3876 target = 0.167926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.129474 restraints weight = 13679.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.129075 restraints weight = 14982.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.130851 restraints weight = 13810.229| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11579 Z= 0.164 Angle : 0.535 7.025 15744 Z= 0.303 Chirality : 0.044 0.152 1772 Planarity : 0.002 0.016 1908 Dihedral : 15.199 138.950 1825 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.82 % Allowed : 19.60 % Favored : 77.58 % 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: -1.30 (0.23), residues: 1292 helix: 0.84 (0.32), residues: 248 sheet: -1.52 (0.24), residues: 436 loop : -0.95 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 228 PHE 0.021 0.001 PHE A 258 TYR 0.012 0.001 TYR D 299 ARG 0.003 0.000 ARG A 286 Details of bonding type rmsd hydrogen bonds : bond 0.03412 ( 416) hydrogen bonds : angle 5.61312 ( 1188) covalent geometry : bond 0.00379 (11579) covalent geometry : angle 0.53489 (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 217 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 182 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6892 (tt0) REVERT: B 313 ARG cc_start: 0.7272 (mtm-85) cc_final: 0.6948 (mtt90) REVERT: B 377 GLU cc_start: 0.8253 (tp30) cc_final: 0.7811 (tp30) REVERT: C 232 ASN cc_start: 0.7866 (t0) cc_final: 0.7598 (p0) REVERT: C 246 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.7320 (mtm-85) REVERT: C 349 ASP cc_start: 0.7346 (m-30) cc_final: 0.7106 (m-30) REVERT: D 106 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7922 (pt0) REVERT: D 186 MET cc_start: 0.7848 (mtm) cc_final: 0.7568 (mtm) outliers start: 35 outliers final: 24 residues processed: 202 average time/residue: 0.2205 time to fit residues: 64.8585 Evaluate side-chains 194 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 1.177 ------------------------------------------------------------------------------- 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 263 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 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 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 185 MET Chi-restraints excluded: chain C residue 246 ARG 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 106 GLN 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: 10.0000 chunk 31 optimal weight: 0.9990 chunk 96 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 270 ASN A 316 ASN B 106 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.170511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.131144 restraints weight = 13599.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.130236 restraints weight = 14228.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.132032 restraints weight = 13267.325| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 11579 Z= 0.296 Angle : 0.660 8.156 15744 Z= 0.366 Chirality : 0.047 0.170 1772 Planarity : 0.003 0.029 1908 Dihedral : 15.481 141.595 1825 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.71 % Allowed : 19.35 % Favored : 76.94 % 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: 0.48 (0.31), residues: 248 sheet: -1.50 (0.24), residues: 464 loop : -1.15 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 228 PHE 0.028 0.002 PHE D 295 TYR 0.018 0.002 TYR D 107 ARG 0.005 0.001 ARG A 286 Details of bonding type rmsd hydrogen bonds : bond 0.04164 ( 416) hydrogen bonds : angle 6.08148 ( 1188) covalent geometry : bond 0.00696 (11579) covalent geometry : angle 0.65967 (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 209 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 163 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 LYS cc_start: 0.8204 (mttt) cc_final: 0.7925 (mttt) REVERT: B 69 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7069 (tt0) REVERT: B 106 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7567 (pp30) REVERT: B 313 ARG cc_start: 0.7316 (mtm-85) cc_final: 0.6862 (mtt90) REVERT: C 156 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8226 (mm) REVERT: C 232 ASN cc_start: 0.7944 (t0) cc_final: 0.7612 (p0) REVERT: C 246 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.7254 (mtm-85) REVERT: C 349 ASP cc_start: 0.7485 (m-30) cc_final: 0.7153 (m-30) REVERT: D 186 MET cc_start: 0.8047 (mtm) cc_final: 0.7787 (mtm) REVERT: D 246 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7320 (mtm-85) outliers start: 46 outliers final: 30 residues processed: 194 average time/residue: 0.2275 time to fit residues: 63.8255 Evaluate side-chains 187 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 1.306 ------------------------------------------------------------------------------- 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 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 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 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 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: 20.0000 chunk 61 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 316 ASN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN ** 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 = 0.4007 r_free = 0.4007 target = 0.181111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.142616 restraints weight = 13211.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.142754 restraints weight = 12789.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.144416 restraints weight = 11979.306| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11579 Z= 0.126 Angle : 0.532 7.497 15744 Z= 0.301 Chirality : 0.043 0.162 1772 Planarity : 0.002 0.019 1908 Dihedral : 15.284 138.415 1825 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.94 % Allowed : 21.37 % Favored : 76.69 % 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: -1.20 (0.23), residues: 1292 helix: 0.91 (0.33), residues: 252 sheet: -1.23 (0.23), residues: 476 loop : -1.05 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 228 PHE 0.017 0.001 PHE A 135 TYR 0.013 0.001 TYR D 299 ARG 0.003 0.000 ARG B 109 Details of bonding type rmsd hydrogen bonds : bond 0.03195 ( 416) hydrogen bonds : angle 5.45572 ( 1188) covalent geometry : bond 0.00280 (11579) covalent geometry : angle 0.53167 (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: 24 poor density : 196 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 106 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7446 (pp30) REVERT: B 313 ARG cc_start: 0.7180 (mtm-85) cc_final: 0.6803 (mtt90) REVERT: B 377 GLU cc_start: 0.8243 (tp30) cc_final: 0.7768 (tp30) REVERT: C 117 TYR cc_start: 0.8362 (p90) cc_final: 0.8107 (p90) REVERT: C 213 LYS cc_start: 0.8402 (mmtm) cc_final: 0.8188 (mmtm) REVERT: C 232 ASN cc_start: 0.7848 (t0) cc_final: 0.7494 (p0) REVERT: C 246 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.7339 (mtm-85) REVERT: C 349 ASP cc_start: 0.7492 (m-30) cc_final: 0.7188 (m-30) outliers start: 24 outliers final: 15 residues processed: 211 average time/residue: 0.2099 time to fit residues: 64.4740 Evaluate side-chains 190 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain D residue 62 THR 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 76 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 113 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 316 ASN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 GLN ** 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 = 0.3936 r_free = 0.3936 target = 0.173593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.134126 restraints weight = 13345.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.133013 restraints weight = 13677.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.134835 restraints weight = 12861.525| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11579 Z= 0.228 Angle : 0.614 8.210 15744 Z= 0.343 Chirality : 0.045 0.163 1772 Planarity : 0.003 0.023 1908 Dihedral : 15.403 140.606 1825 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.02 % Allowed : 21.61 % Favored : 76.37 % 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: -1.36 (0.23), residues: 1292 helix: 0.77 (0.32), residues: 248 sheet: -1.44 (0.25), residues: 420 loop : -1.10 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 228 PHE 0.025 0.002 PHE A 135 TYR 0.022 0.002 TYR D 107 ARG 0.004 0.001 ARG A 286 Details of bonding type rmsd hydrogen bonds : bond 0.03731 ( 416) hydrogen bonds : angle 5.81504 ( 1188) covalent geometry : bond 0.00533 (11579) covalent geometry : angle 0.61352 (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 190 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 TYR cc_start: 0.7192 (t80) cc_final: 0.6959 (t80) REVERT: A 213 LYS cc_start: 0.8421 (mmtm) cc_final: 0.8205 (mmtp) REVERT: B 313 ARG cc_start: 0.7260 (mtm-85) cc_final: 0.6838 (mtt90) REVERT: B 377 GLU cc_start: 0.8314 (tp30) cc_final: 0.7654 (tp30) REVERT: C 55 LYS cc_start: 0.8739 (ttmt) cc_final: 0.8512 (ttmt) REVERT: C 156 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8263 (mm) REVERT: C 232 ASN cc_start: 0.7900 (t0) cc_final: 0.7609 (p0) REVERT: C 246 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.7204 (mtm-85) REVERT: C 349 ASP cc_start: 0.7548 (m-30) cc_final: 0.7239 (m-30) outliers start: 25 outliers final: 19 residues processed: 181 average time/residue: 0.2077 time to fit residues: 55.7670 Evaluate side-chains 178 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET 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 329 LEU Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 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 C residue 156 ILE Chi-restraints excluded: chain C residue 246 ARG 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 308 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 122 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 20.0000 chunk 10 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 316 ASN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** 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 = 0.3977 r_free = 0.3977 target = 0.177726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.139915 restraints weight = 13232.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.140096 restraints weight = 12688.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.141622 restraints weight = 11915.240| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11579 Z= 0.131 Angle : 0.537 7.753 15744 Z= 0.304 Chirality : 0.044 0.159 1772 Planarity : 0.002 0.018 1908 Dihedral : 15.227 138.976 1825 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.94 % Allowed : 21.69 % Favored : 76.37 % 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: -1.12 (0.23), residues: 1292 helix: 0.86 (0.33), residues: 252 sheet: -1.09 (0.23), residues: 484 loop : -1.04 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 228 PHE 0.020 0.001 PHE A 135 TYR 0.014 0.001 TYR D 107 ARG 0.003 0.000 ARG A 268 Details of bonding type rmsd hydrogen bonds : bond 0.03270 ( 416) hydrogen bonds : angle 5.48748 ( 1188) covalent geometry : bond 0.00293 (11579) covalent geometry : angle 0.53682 (15744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3148.86 seconds wall clock time: 56 minutes 33.47 seconds (3393.47 seconds total)