Starting phenix.real_space_refine on Sun Dec 29 19:04:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ypo_34010/12_2024/7ypo_34010.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ypo_34010/12_2024/7ypo_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_34010/12_2024/7ypo_34010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ypo_34010/12_2024/7ypo_34010.map" model { file = "/net/cci-nas-00/data/ceres_data/7ypo_34010/12_2024/7ypo_34010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ypo_34010/12_2024/7ypo_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-5532/modules/chem_data/mon_lib" Total number of atoms: 11324 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2684 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 324} Chain breaks: 1 Chain: "B" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2684 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 324} Chain breaks: 1 Chain: "C" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2684 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 324} Chain breaks: 1 Chain: "D" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2684 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 324} Chain breaks: 1 Chain: "Q" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 588 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Time building chain proxies: 7.39, per 1000 atoms: 0.65 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: 2.61 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: 3.59 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: 3.83 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3607 1.34 - 1.46: 2568 1.46 - 1.57: 5273 1.57 - 1.69: 55 1.69 - 1.81: 76 Bond restraints: 11579 Sorted by residual: bond pdb=" CZ ARG C 313 " pdb=" NH2 ARG C 313 " ideal model delta sigma weight residual 1.330 1.317 0.013 1.30e-02 5.92e+03 1.03e+00 bond pdb=" CZ ARG D 313 " pdb=" NH2 ARG D 313 " ideal model delta sigma weight residual 1.330 1.317 0.013 1.30e-02 5.92e+03 1.03e+00 bond pdb=" CZ ARG B 313 " pdb=" NH2 ARG B 313 " ideal model delta sigma weight residual 1.330 1.317 0.013 1.30e-02 5.92e+03 1.01e+00 bond pdb=" C4' DA Q 26 " pdb=" O4' DA Q 26 " ideal model delta sigma weight residual 1.450 1.430 0.020 2.00e-02 2.50e+03 9.93e-01 bond pdb=" CZ ARG A 313 " pdb=" NH2 ARG A 313 " ideal model delta sigma weight residual 1.330 1.318 0.012 1.30e-02 5.92e+03 9.02e-01 ... (remaining 11574 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 14956 1.21 - 2.42: 668 2.42 - 3.63: 100 3.63 - 4.83: 16 4.83 - 6.04: 4 Bond angle restraints: 15744 Sorted by residual: angle pdb=" C ARG B 109 " pdb=" N LYS B 110 " pdb=" CA LYS B 110 " ideal model delta sigma weight residual 121.54 127.58 -6.04 1.91e+00 2.74e-01 1.00e+01 angle pdb=" C ARG A 109 " pdb=" N LYS A 110 " pdb=" CA LYS A 110 " ideal model delta sigma weight residual 121.54 127.56 -6.02 1.91e+00 2.74e-01 9.92e+00 angle pdb=" C ARG D 109 " pdb=" N LYS D 110 " pdb=" CA LYS D 110 " ideal model delta sigma weight residual 121.54 127.55 -6.01 1.91e+00 2.74e-01 9.90e+00 angle pdb=" C ARG C 109 " pdb=" N LYS C 110 " pdb=" CA LYS C 110 " ideal model delta sigma weight residual 121.54 127.55 -6.01 1.91e+00 2.74e-01 9.89e+00 angle pdb=" C ILE B 66 " pdb=" N ASN B 67 " pdb=" CA ASN B 67 " ideal model delta sigma weight residual 122.82 126.13 -3.31 1.42e+00 4.96e-01 5.42e+00 ... (remaining 15739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.29: 6569 28.29 - 56.59: 406 56.59 - 84.88: 25 84.88 - 113.17: 4 113.17 - 141.46: 1 Dihedral angle restraints: 7005 sinusoidal: 3077 harmonic: 3928 Sorted by residual: dihedral pdb=" C4' DA Q 17 " pdb=" C3' DA Q 17 " pdb=" O3' DA Q 17 " pdb=" P DA Q 18 " ideal model delta sinusoidal sigma weight residual 220.00 78.54 141.46 1 3.50e+01 8.16e-04 1.40e+01 dihedral pdb=" CA ASN D 303 " pdb=" C ASN D 303 " pdb=" N GLU D 304 " pdb=" CA GLU D 304 " ideal model delta harmonic sigma weight residual -180.00 -162.39 -17.61 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ASN C 303 " pdb=" C ASN C 303 " pdb=" N GLU C 304 " pdb=" CA GLU C 304 " ideal model delta harmonic sigma weight residual -180.00 -162.40 -17.60 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 7002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1053 0.029 - 0.059: 426 0.059 - 0.088: 167 0.088 - 0.117: 99 0.117 - 0.147: 27 Chirality restraints: 1772 Sorted by residual: chirality pdb=" CA ILE B 83 " pdb=" N ILE B 83 " pdb=" C ILE B 83 " pdb=" CB ILE B 83 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.38e-01 chirality pdb=" CA ILE A 83 " pdb=" N ILE A 83 " pdb=" C ILE A 83 " pdb=" CB ILE A 83 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA ILE D 83 " pdb=" N ILE D 83 " pdb=" C ILE D 83 " pdb=" CB ILE D 83 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.25e-01 ... (remaining 1769 not shown) Planarity restraints: 1908 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 152 " -0.007 2.00e-02 2.50e+03 6.35e-03 8.06e-01 pdb=" CG TYR B 152 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR B 152 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 152 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 152 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 152 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 152 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 152 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 152 " -0.007 2.00e-02 2.50e+03 6.15e-03 7.58e-01 pdb=" CG TYR A 152 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR A 152 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 152 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 152 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 152 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 152 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 152 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 152 " 0.007 2.00e-02 2.50e+03 6.09e-03 7.42e-01 pdb=" CG TYR D 152 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR D 152 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR D 152 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR D 152 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR D 152 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 152 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 152 " 0.001 2.00e-02 2.50e+03 ... (remaining 1905 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 172 2.65 - 3.21: 10736 3.21 - 3.78: 16580 3.78 - 4.34: 23545 4.34 - 4.90: 38894 Nonbonded interactions: 89927 Sorted by model distance: nonbonded pdb=" OD1 ASP D 188 " pdb=" N PHE D 189 " model vdw 2.091 3.120 nonbonded pdb=" OD1 ASP C 188 " pdb=" N PHE C 189 " model vdw 2.091 3.120 nonbonded pdb=" OD1 ASP B 188 " pdb=" N PHE B 189 " model vdw 2.091 3.120 nonbonded pdb=" OD1 ASP A 188 " pdb=" N PHE A 189 " model vdw 2.091 3.120 nonbonded pdb=" NE2 GLN A 119 " pdb=" O CYS A 120 " model vdw 2.241 3.120 ... (remaining 89922 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.340 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.660 ------------------------------------------------------------------------------- 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= 0.239 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 *********************** 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 : 1.283 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: 0.1915 time to fit residues: 69.5724 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 : 1.417 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 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= 0.374 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 *********************** 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 : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 ARG cc_start: 0.7222 (mtt90) cc_final: 0.6976 (mtt-85) REVERT: C 55 LYS cc_start: 0.8846 (ttmt) cc_final: 0.8551 (tttt) REVERT: C 190 LYS cc_start: 0.7993 (ptpp) cc_final: 0.7733 (ptpp) REVERT: C 349 ASP cc_start: 0.7511 (m-30) cc_final: 0.7266 (m-30) REVERT: D 68 ASN cc_start: 0.7107 (m110) cc_final: 0.6888 (m110) REVERT: D 186 MET cc_start: 0.7780 (mtm) cc_final: 0.7517 (mtm) outliers start: 23 outliers final: 16 residues processed: 206 average time/residue: 0.2087 time to fit residues: 63.3018 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 : 1.355 ------------------------------------------------------------------------------- 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 65 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 80 optimal weight: 0.1980 chunk 32 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 117 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11579 Z= 0.167 Angle : 0.510 6.534 15744 Z= 0.293 Chirality : 0.043 0.146 1772 Planarity : 0.002 0.018 1908 Dihedral : 15.095 136.416 1825 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.37 % Allowed : 15.73 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.37 (0.23), residues: 1292 helix: 0.72 (0.32), residues: 252 sheet: -1.41 (0.23), residues: 480 loop : -1.05 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 228 PHE 0.022 0.001 PHE A 258 TYR 0.014 0.001 TYR A 289 ARG 0.002 0.000 ARG C 286 *********************** 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 238 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 221 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.6857 (tptt) cc_final: 0.6263 (tptp) REVERT: A 149 LYS cc_start: 0.8173 (tttp) cc_final: 0.7867 (tttp) REVERT: A 209 ASP cc_start: 0.6946 (t0) cc_final: 0.6718 (t0) REVERT: C 117 TYR cc_start: 0.8295 (p90) cc_final: 0.7989 (p90) REVERT: C 342 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7385 (tm-30) REVERT: C 349 ASP cc_start: 0.7398 (m-30) cc_final: 0.7138 (m-30) REVERT: D 186 MET cc_start: 0.7554 (mtm) cc_final: 0.7290 (mtm) outliers start: 17 outliers final: 9 residues processed: 228 average time/residue: 0.2198 time to fit residues: 73.5494 Evaluate side-chains 200 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 191 time to evaluate : 1.203 ------------------------------------------------------------------------------- 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 288 ILE Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain D residue 62 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 116 optimal weight: 20.0000 chunk 88 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 chunk 125 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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** A 316 ASN ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 11579 Z= 0.319 Angle : 0.579 5.890 15744 Z= 0.327 Chirality : 0.045 0.169 1772 Planarity : 0.003 0.022 1908 Dihedral : 15.206 139.173 1825 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.94 % Allowed : 17.82 % Favored : 80.24 % 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: -1.37 (0.23), residues: 1292 helix: 0.71 (0.31), residues: 248 sheet: -1.46 (0.23), residues: 480 loop : -0.97 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 228 PHE 0.025 0.002 PHE C 135 TYR 0.017 0.002 TYR B 163 ARG 0.004 0.001 ARG B 286 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 TYR cc_start: 0.7246 (t80) cc_final: 0.7041 (t80) REVERT: A 209 ASP cc_start: 0.7302 (t0) cc_final: 0.7020 (t0) REVERT: B 313 ARG cc_start: 0.6961 (mtm-85) cc_final: 0.6708 (mtt-85) REVERT: C 156 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8253 (mm) REVERT: C 342 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7366 (tm-30) REVERT: D 186 MET cc_start: 0.7665 (mtm) cc_final: 0.7369 (mtm) outliers start: 24 outliers final: 17 residues processed: 205 average time/residue: 0.2279 time to fit residues: 68.1892 Evaluate side-chains 186 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 1.249 ------------------------------------------------------------------------------- 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 B residue 127 MET 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 90 THR Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 128 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 104 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 64 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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** A 316 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 ASN ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2652 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= 0.274 Angle : 0.552 6.873 15744 Z= 0.313 Chirality : 0.044 0.156 1772 Planarity : 0.003 0.018 1908 Dihedral : 15.160 138.512 1825 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.15 % Allowed : 18.71 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.29 (0.23), residues: 1292 helix: 0.86 (0.31), residues: 248 sheet: -1.42 (0.23), residues: 480 loop : -0.96 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 228 PHE 0.020 0.002 PHE A 135 TYR 0.015 0.001 TYR D 299 ARG 0.003 0.000 ARG A 286 *********************** 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: 39 poor density : 189 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6609 (tt0) REVERT: B 106 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7310 (pp30) REVERT: B 313 ARG cc_start: 0.7029 (mtm-85) cc_final: 0.6703 (mtt90) REVERT: C 156 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8250 (mm) REVERT: C 342 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7368 (tm-30) REVERT: D 106 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7520 (pp30) REVERT: D 186 MET cc_start: 0.7660 (mtm) cc_final: 0.7328 (mtm) outliers start: 39 outliers final: 23 residues processed: 211 average time/residue: 0.2192 time to fit residues: 67.8300 Evaluate side-chains 195 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 1.389 ------------------------------------------------------------------------------- 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 339 SER Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 156 ILE 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 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 106 GLN Chi-restraints excluded: chain D residue 128 THR 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 42 optimal weight: 0.9980 chunk 113 optimal weight: 0.3980 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 67 ASN A 106 GLN A 316 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11579 Z= 0.253 Angle : 0.537 6.637 15744 Z= 0.305 Chirality : 0.044 0.153 1772 Planarity : 0.002 0.017 1908 Dihedral : 15.185 138.827 1825 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.66 % Allowed : 19.60 % Favored : 77.74 % 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: -1.23 (0.23), residues: 1292 helix: 1.06 (0.32), residues: 248 sheet: -1.51 (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 D 228 PHE 0.028 0.001 PHE C 135 TYR 0.016 0.001 TYR A 299 ARG 0.003 0.000 ARG B 268 *********************** 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 220 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 TYR cc_start: 0.7156 (t80) cc_final: 0.6943 (t80) REVERT: B 106 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7335 (pp30) REVERT: B 313 ARG cc_start: 0.7098 (mtm-85) cc_final: 0.6754 (mtt90) REVERT: C 342 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7389 (tm-30) REVERT: D 106 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7461 (pp30) REVERT: D 186 MET cc_start: 0.7626 (mtm) cc_final: 0.7281 (mtm) outliers start: 33 outliers final: 22 residues processed: 208 average time/residue: 0.2219 time to fit residues: 67.9155 Evaluate side-chains 196 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 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 185 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 A 316 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 ASN ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11579 Z= 0.316 Angle : 0.589 7.905 15744 Z= 0.329 Chirality : 0.044 0.173 1772 Planarity : 0.003 0.020 1908 Dihedral : 15.223 139.814 1825 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.58 % Allowed : 20.56 % Favored : 76.85 % 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: -1.27 (0.23), residues: 1292 helix: 1.00 (0.32), residues: 248 sheet: -1.54 (0.24), residues: 436 loop : -0.96 (0.25), residues: 608 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 A 299 ARG 0.005 0.001 ARG A 313 *********************** 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 207 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 TYR cc_start: 0.7239 (t80) cc_final: 0.6997 (t80) REVERT: B 69 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6625 (tt0) REVERT: B 106 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7358 (pp30) REVERT: B 313 ARG cc_start: 0.7104 (mtm-85) cc_final: 0.6745 (mtt90) REVERT: C 156 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8260 (mm) REVERT: D 106 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7894 (pt0) REVERT: D 186 MET cc_start: 0.7702 (mtm) cc_final: 0.7368 (mtm) REVERT: D 253 MET cc_start: 0.6647 (tpt) cc_final: 0.6407 (tpt) outliers start: 32 outliers final: 24 residues processed: 196 average time/residue: 0.2152 time to fit residues: 61.9928 Evaluate side-chains 192 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 156 ILE 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 156 ILE Chi-restraints excluded: chain C residue 185 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 106 GLN Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 308 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 120 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 79 ASN A 106 GLN A 316 ASN C 98 ASN ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11579 Z= 0.167 Angle : 0.520 7.407 15744 Z= 0.293 Chirality : 0.043 0.162 1772 Planarity : 0.002 0.019 1908 Dihedral : 15.146 137.709 1825 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.61 % Allowed : 21.61 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.23), residues: 1292 helix: 1.15 (0.33), residues: 252 sheet: -1.18 (0.23), residues: 476 loop : -0.87 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 228 PHE 0.015 0.001 PHE A 135 TYR 0.014 0.001 TYR A 299 ARG 0.004 0.000 ARG B 268 *********************** 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 231 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 211 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.7224 (t0) cc_final: 0.6487 (t0) REVERT: B 106 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7242 (pp30) REVERT: B 164 LYS cc_start: 0.8363 (ttmt) cc_final: 0.7987 (ttmt) REVERT: B 313 ARG cc_start: 0.7122 (mtm-85) cc_final: 0.6755 (mtt90) REVERT: C 117 TYR cc_start: 0.8294 (p90) cc_final: 0.8059 (p90) REVERT: C 246 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7341 (mtm-85) REVERT: D 106 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7746 (pt0) REVERT: D 186 MET cc_start: 0.7468 (mtm) cc_final: 0.7120 (mtm) outliers start: 20 outliers final: 11 residues processed: 222 average time/residue: 0.2318 time to fit residues: 74.1452 Evaluate side-chains 195 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 181 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 106 GLN 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 279 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 257 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 120 optimal weight: 0.9980 chunk 70 optimal weight: 0.3980 chunk 50 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 105 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- 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 A 316 ASN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11579 Z= 0.348 Angle : 0.617 7.519 15744 Z= 0.345 Chirality : 0.045 0.163 1772 Planarity : 0.003 0.024 1908 Dihedral : 15.230 140.324 1825 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.34 % Allowed : 21.45 % Favored : 76.21 % 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: -1.22 (0.23), residues: 1292 helix: 0.83 (0.32), residues: 248 sheet: -1.38 (0.23), residues: 468 loop : -0.89 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 228 PHE 0.024 0.002 PHE B 295 TYR 0.018 0.002 TYR B 157 ARG 0.004 0.001 ARG B 286 *********************** 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 204 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 TYR cc_start: 0.7255 (t80) cc_final: 0.6995 (t80) REVERT: A 164 LYS cc_start: 0.8349 (ttmt) cc_final: 0.8139 (ttmt) REVERT: A 209 ASP cc_start: 0.7451 (t0) cc_final: 0.6355 (t0) REVERT: B 106 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7375 (pp30) REVERT: B 313 ARG cc_start: 0.7117 (mtm-85) cc_final: 0.6770 (mtt90) REVERT: C 246 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.7244 (mtm-85) REVERT: C 349 ASP cc_start: 0.7440 (m-30) cc_final: 0.7179 (m-30) REVERT: D 106 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7751 (pt0) REVERT: D 186 MET cc_start: 0.7711 (mtm) cc_final: 0.7402 (mtm) outliers start: 29 outliers final: 17 residues processed: 196 average time/residue: 0.2281 time to fit residues: 65.4898 Evaluate side-chains 184 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 106 GLN 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 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 106 GLN Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 308 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 129 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 316 ASN B 79 ASN B 228 HIS ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11579 Z= 0.269 Angle : 0.584 8.683 15744 Z= 0.329 Chirality : 0.045 0.158 1772 Planarity : 0.003 0.045 1908 Dihedral : 15.166 139.852 1825 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.10 % Allowed : 21.69 % Favored : 76.21 % 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: -1.21 (0.23), residues: 1292 helix: 0.83 (0.32), residues: 248 sheet: -1.25 (0.23), residues: 476 loop : -0.98 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 228 PHE 0.022 0.001 PHE A 135 TYR 0.018 0.001 TYR A 212 ARG 0.007 0.001 ARG A 313 ********************** 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 191 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 TYR cc_start: 0.7187 (t80) cc_final: 0.6936 (t80) REVERT: B 106 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7325 (pp30) REVERT: B 313 ARG cc_start: 0.7125 (mtm-85) cc_final: 0.6774 (mtt90) REVERT: B 342 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7222 (tm-30) REVERT: C 246 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.7243 (mtm-85) REVERT: C 349 ASP cc_start: 0.7459 (m-30) cc_final: 0.7194 (m-30) REVERT: D 106 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7707 (pt0) REVERT: D 186 MET cc_start: 0.7499 (mtm) cc_final: 0.7213 (mtm) outliers start: 26 outliers final: 20 residues processed: 183 average time/residue: 0.2279 time to fit residues: 60.7762 Evaluate side-chains 179 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 263 THR 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 228 HIS 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 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 106 GLN Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 308 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 0.0370 chunk 90 optimal weight: 0.2980 chunk 5 optimal weight: 5.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 316 ASN B 228 HIS ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.178812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.140545 restraints weight = 13088.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.140366 restraints weight = 11753.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.142301 restraints weight = 11357.183| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3439 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= 0.169 Angle : 0.533 7.783 15744 Z= 0.301 Chirality : 0.044 0.159 1772 Planarity : 0.003 0.042 1908 Dihedral : 15.062 138.328 1825 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.69 % Allowed : 21.85 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.23), residues: 1292 helix: 0.97 (0.32), residues: 252 sheet: -1.09 (0.23), residues: 476 loop : -0.91 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS B 228 PHE 0.018 0.001 PHE A 135 TYR 0.013 0.001 TYR D 107 ARG 0.007 0.001 ARG A 313 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2241.02 seconds wall clock time: 42 minutes 42.81 seconds (2562.81 seconds total)