Starting phenix.real_space_refine on Wed May 14 12:07:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ewq_50022/05_2025/9ewq_50022.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ewq_50022/05_2025/9ewq_50022.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ewq_50022/05_2025/9ewq_50022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ewq_50022/05_2025/9ewq_50022.map" model { file = "/net/cci-nas-00/data/ceres_data/9ewq_50022/05_2025/9ewq_50022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ewq_50022/05_2025/9ewq_50022.cif" } resolution = 3.0 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= 0.000 sd= 0.059 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 7480 2.51 5 N 2044 2.21 5 O 2296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11904 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2976 Classifications: {'peptide': 385} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 363} Chain: "B" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2976 Classifications: {'peptide': 385} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 363} Chain: "C" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2976 Classifications: {'peptide': 385} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 363} Chain: "D" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2976 Classifications: {'peptide': 385} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 363} Time building chain proxies: 8.10, per 1000 atoms: 0.68 Number of scatterers: 11904 At special positions: 0 Unit cell: (117.633, 117.633, 65.583, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2296 8.00 N 2044 7.00 C 7480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 34 " - pdb=" SG CYS A 39 " distance=2.03 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 143 " - pdb=" SG CYS A 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 200 " distance=2.03 Simple disulfide: pdb=" SG CYS B 34 " - pdb=" SG CYS B 39 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 141 " distance=2.02 Simple disulfide: pdb=" SG CYS B 143 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 202 " distance=2.03 Simple disulfide: pdb=" SG CYS B 191 " - pdb=" SG CYS B 200 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 356 " distance=2.03 Simple disulfide: pdb=" SG CYS C 34 " - pdb=" SG CYS C 39 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 141 " distance=2.02 Simple disulfide: pdb=" SG CYS C 143 " - pdb=" SG CYS C 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 189 " - pdb=" SG CYS C 202 " distance=2.03 Simple disulfide: pdb=" SG CYS C 191 " - pdb=" SG CYS C 200 " distance=2.03 Simple disulfide: pdb=" SG CYS D 34 " - pdb=" SG CYS D 39 " distance=2.03 Simple disulfide: pdb=" SG CYS D 94 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 143 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS D 189 " - pdb=" SG CYS D 202 " distance=2.03 Simple disulfide: pdb=" SG CYS D 191 " - pdb=" SG CYS D 200 " distance=2.03 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 356 " distance=2.04 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: 2.92 Conformation dependent library (CDL) restraints added in 1.6 seconds 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2760 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 27 sheets defined 4.4% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 14 through 19 Processing helix chain 'A' and resid 52 through 56 removed outlier: 3.624A pdb=" N ASN A 56 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'B' and resid 14 through 19 Processing helix chain 'B' and resid 52 through 56 removed outlier: 3.599A pdb=" N ASN B 56 " --> pdb=" O LYS B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 324 Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 52 through 56 removed outlier: 3.690A pdb=" N ASN C 56 " --> pdb=" O LYS C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 324 Processing helix chain 'D' and resid 14 through 19 Processing helix chain 'D' and resid 52 through 56 removed outlier: 3.665A pdb=" N ASN D 56 " --> pdb=" O LYS D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 324 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 13 removed outlier: 6.483A pdb=" N SER A 354 " --> pdb=" O TYR A 10 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LYS A 12 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N SER A 352 " --> pdb=" O LYS A 12 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 34 removed outlier: 6.649A pdb=" N LEU A 68 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 95 removed outlier: 3.573A pdb=" N SER A 90 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 113 " --> pdb=" O SER A 106 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP A 124 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N TYR A 118 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ILE A 122 " --> pdb=" O TYR A 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 144 removed outlier: 3.533A pdb=" N ALA A 142 " --> pdb=" O PHE A 149 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS A 175 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLU A 169 " --> pdb=" O ILE A 173 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ILE A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 190 through 194 Processing sheet with id=AA6, first strand: chain 'A' and resid 262 through 263 removed outlier: 3.909A pdb=" N GLY A 266 " --> pdb=" O TYR A 263 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS A 279 " --> pdb=" O GLY A 305 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N GLY A 305 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N PHE A 281 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 299 " --> pdb=" O TRP A 285 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 6 through 13 removed outlier: 6.583A pdb=" N SER B 354 " --> pdb=" O TYR B 10 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LYS B 12 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N SER B 352 " --> pdb=" O LYS B 12 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 31 through 34 removed outlier: 6.298A pdb=" N SER B 70 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N PHE B 84 " --> pdb=" O SER B 70 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 90 through 95 removed outlier: 3.552A pdb=" N SER B 90 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL B 113 " --> pdb=" O SER B 106 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA B 114 " --> pdb=" O THR B 125 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR B 125 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU B 116 " --> pdb=" O THR B 123 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 134 through 135 removed outlier: 3.529A pdb=" N ALA B 142 " --> pdb=" O PHE B 149 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 134 through 135 removed outlier: 3.702A pdb=" N LYS B 175 " --> pdb=" O ARG B 167 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLU B 169 " --> pdb=" O ILE B 173 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ILE B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 190 through 193 Processing sheet with id=AB4, first strand: chain 'B' and resid 262 through 263 removed outlier: 3.859A pdb=" N GLY B 266 " --> pdb=" O TYR B 263 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS B 279 " --> pdb=" O GLY B 305 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLY B 305 " --> pdb=" O LYS B 279 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHE B 281 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 299 " --> pdb=" O TRP B 285 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 6 through 13 removed outlier: 6.496A pdb=" N SER C 354 " --> pdb=" O TYR C 10 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LYS C 12 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N SER C 352 " --> pdb=" O LYS C 12 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 31 through 34 removed outlier: 6.289A pdb=" N SER C 70 " --> pdb=" O PHE C 84 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N PHE C 84 " --> pdb=" O SER C 70 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 90 through 95 removed outlier: 3.534A pdb=" N SER C 90 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL C 113 " --> pdb=" O SER C 106 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA C 114 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N THR C 125 " --> pdb=" O ALA C 114 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU C 116 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 134 through 135 removed outlier: 3.537A pdb=" N ALA C 142 " --> pdb=" O PHE C 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 134 through 135 removed outlier: 4.702A pdb=" N TYR C 163 " --> pdb=" O MET C 179 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS C 175 " --> pdb=" O ARG C 167 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU C 169 " --> pdb=" O ILE C 173 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ILE C 173 " --> pdb=" O GLU C 169 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 190 through 193 Processing sheet with id=AC2, first strand: chain 'C' and resid 262 through 263 removed outlier: 3.772A pdb=" N GLY C 266 " --> pdb=" O TYR C 263 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LYS C 279 " --> pdb=" O GLY C 305 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N GLY C 305 " --> pdb=" O LYS C 279 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N PHE C 281 " --> pdb=" O ILE C 303 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE C 299 " --> pdb=" O TRP C 285 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 6 through 13 removed outlier: 6.576A pdb=" N SER D 354 " --> pdb=" O TYR D 10 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYS D 12 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N SER D 352 " --> pdb=" O LYS D 12 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 31 through 34 removed outlier: 6.617A pdb=" N LEU D 68 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 90 through 95 removed outlier: 3.601A pdb=" N SER D 90 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL D 113 " --> pdb=" O SER D 106 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP D 124 " --> pdb=" O LEU D 116 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR D 118 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ILE D 122 " --> pdb=" O TYR D 118 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 134 through 135 removed outlier: 3.540A pdb=" N ALA D 142 " --> pdb=" O PHE D 149 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 134 through 135 removed outlier: 3.604A pdb=" N LYS D 175 " --> pdb=" O ARG D 167 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLU D 169 " --> pdb=" O ILE D 173 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ILE D 173 " --> pdb=" O GLU D 169 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 190 through 194 Processing sheet with id=AC9, first strand: chain 'D' and resid 267 through 271 removed outlier: 6.636A pdb=" N LYS D 279 " --> pdb=" O GLY D 305 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLY D 305 " --> pdb=" O LYS D 279 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N PHE D 281 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE D 299 " --> pdb=" O TRP D 285 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 975 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.87 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3881 1.34 - 1.46: 3048 1.46 - 1.58: 5203 1.58 - 1.70: 0 1.70 - 1.82: 100 Bond restraints: 12232 Sorted by residual: bond pdb=" C ARG A 340 " pdb=" N PRO A 341 " ideal model delta sigma weight residual 1.335 1.352 -0.018 1.28e-02 6.10e+03 1.91e+00 bond pdb=" C ARG C 340 " pdb=" N PRO C 341 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.19e-02 7.06e+03 1.87e+00 bond pdb=" C ARG B 340 " pdb=" N PRO B 341 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.36e-02 5.41e+03 1.85e+00 bond pdb=" CG PRO B 236 " pdb=" CD PRO B 236 " ideal model delta sigma weight residual 1.512 1.479 0.033 2.70e-02 1.37e+03 1.53e+00 bond pdb=" CG PRO A 374 " pdb=" CD PRO A 374 " ideal model delta sigma weight residual 1.512 1.482 0.030 2.70e-02 1.37e+03 1.20e+00 ... (remaining 12227 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 15983 1.26 - 2.52: 524 2.52 - 3.78: 98 3.78 - 5.04: 13 5.04 - 6.30: 6 Bond angle restraints: 16624 Sorted by residual: angle pdb=" CA CYS D 228 " pdb=" C CYS D 228 " pdb=" N SER D 229 " ideal model delta sigma weight residual 114.60 118.24 -3.64 1.30e+00 5.92e-01 7.84e+00 angle pdb=" CA CYS C 228 " pdb=" C CYS C 228 " pdb=" N SER C 229 " ideal model delta sigma weight residual 114.60 118.20 -3.60 1.30e+00 5.92e-01 7.69e+00 angle pdb=" N GLY B 230 " pdb=" CA GLY B 230 " pdb=" C GLY B 230 " ideal model delta sigma weight residual 115.32 112.30 3.02 1.31e+00 5.83e-01 5.32e+00 angle pdb=" CA CYS D 228 " pdb=" C CYS D 228 " pdb=" O CYS D 228 " ideal model delta sigma weight residual 122.63 119.73 2.90 1.29e+00 6.01e-01 5.04e+00 angle pdb=" N ASN C 254 " pdb=" CA ASN C 254 " pdb=" C ASN C 254 " ideal model delta sigma weight residual 110.80 106.03 4.77 2.13e+00 2.20e-01 5.02e+00 ... (remaining 16619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.32: 6318 16.32 - 32.64: 687 32.64 - 48.96: 132 48.96 - 65.28: 33 65.28 - 81.60: 12 Dihedral angle restraints: 7182 sinusoidal: 2838 harmonic: 4344 Sorted by residual: dihedral pdb=" CB CYS D 94 " pdb=" SG CYS D 94 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 173.64 -80.64 1 1.00e+01 1.00e-02 8.04e+01 dihedral pdb=" CB CYS A 94 " pdb=" SG CYS A 94 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 171.84 -78.84 1 1.00e+01 1.00e-02 7.74e+01 dihedral pdb=" CB CYS C 94 " pdb=" SG CYS C 94 " pdb=" SG CYS C 141 " pdb=" CB CYS C 141 " ideal model delta sinusoidal sigma weight residual 93.00 168.20 -75.20 1 1.00e+01 1.00e-02 7.15e+01 ... (remaining 7179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 978 0.033 - 0.065: 472 0.065 - 0.097: 146 0.097 - 0.130: 138 0.130 - 0.162: 2 Chirality restraints: 1736 Sorted by residual: chirality pdb=" CA ILE C 133 " pdb=" N ILE C 133 " pdb=" C ILE C 133 " pdb=" CB ILE C 133 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.60e-01 chirality pdb=" CB ILE D 9 " pdb=" CA ILE D 9 " pdb=" CG1 ILE D 9 " pdb=" CG2 ILE D 9 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA ILE C 165 " pdb=" N ILE C 165 " pdb=" C ILE C 165 " pdb=" CB ILE C 165 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 1733 not shown) Planarity restraints: 2168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 35 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO D 36 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO D 36 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 36 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 329 " -0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO C 330 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO C 330 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 330 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 235 " -0.023 5.00e-02 4.00e+02 3.47e-02 1.92e+00 pdb=" N PRO C 236 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " -0.020 5.00e-02 4.00e+02 ... (remaining 2165 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 363 2.69 - 3.24: 10502 3.24 - 3.80: 18422 3.80 - 4.35: 26644 4.35 - 4.90: 47549 Nonbonded interactions: 103480 Sorted by model distance: nonbonded pdb=" OD2 ASP B 13 " pdb=" OG SER B 15 " model vdw 2.141 3.040 nonbonded pdb=" OD2 ASP A 204 " pdb=" OH TYR A 226 " model vdw 2.174 3.040 nonbonded pdb=" OD2 ASP C 204 " pdb=" OH TYR C 226 " model vdw 2.176 3.040 nonbonded pdb=" OD2 ASP D 204 " pdb=" OH TYR D 226 " model vdw 2.187 3.040 nonbonded pdb=" O ASP B 13 " pdb=" OG SER B 351 " model vdw 2.192 3.040 ... (remaining 103475 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: 0.03 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 individual isotropic 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: 4.320 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: 30.200 Find NCS groups from input model: 0.410 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: 0.000 Load rotamer database and sin/cos tables:11.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 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 0.048 12254 Z= 0.181 Angle : 0.573 6.295 16668 Z= 0.311 Chirality : 0.048 0.162 1736 Planarity : 0.004 0.039 2168 Dihedral : 13.591 81.598 4356 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.08 % Allowed : 0.38 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.21), residues: 1532 helix: -2.81 (0.82), residues: 24 sheet: 0.01 (0.22), residues: 564 loop : -1.47 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 89 HIS 0.007 0.001 HIS C 207 PHE 0.015 0.002 PHE B 316 TYR 0.007 0.001 TYR A 184 ARG 0.006 0.000 ARG D 203 Details of bonding type rmsd hydrogen bonds : bond 0.18479 ( 360) hydrogen bonds : angle 8.83289 ( 975) SS BOND : bond 0.00358 ( 22) SS BOND : angle 0.73655 ( 44) covalent geometry : bond 0.00448 (12232) covalent geometry : angle 0.57265 (16624) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 1.328 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 100 average time/residue: 1.2317 time to fit residues: 134.5526 Evaluate side-chains 79 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 0.3980 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 0.0170 chunk 72 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 overall best weight: 0.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN C 205 ASN D 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.089283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.079418 restraints weight = 15330.947| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 1.34 r_work: 0.2640 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.0706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12254 Z= 0.136 Angle : 0.547 5.560 16668 Z= 0.295 Chirality : 0.047 0.163 1736 Planarity : 0.004 0.044 2168 Dihedral : 4.709 20.143 1652 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.68 % Allowed : 5.20 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % 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: -1.16 (0.21), residues: 1532 helix: -2.68 (0.82), residues: 24 sheet: 0.28 (0.23), residues: 544 loop : -1.42 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 89 HIS 0.004 0.001 HIS C 207 PHE 0.019 0.002 PHE C 316 TYR 0.009 0.001 TYR B 163 ARG 0.004 0.000 ARG D 203 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 360) hydrogen bonds : angle 6.72288 ( 975) SS BOND : bond 0.00241 ( 22) SS BOND : angle 1.00398 ( 44) covalent geometry : bond 0.00336 (12232) covalent geometry : angle 0.54556 (16624) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 1.329 Fit side-chains revert: symmetry clash REVERT: C 46 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7308 (mt0) REVERT: C 249 SER cc_start: 0.8010 (t) cc_final: 0.7745 (m) REVERT: C 302 ASP cc_start: 0.8836 (m-30) cc_final: 0.8544 (m-30) outliers start: 9 outliers final: 2 residues processed: 98 average time/residue: 1.3405 time to fit residues: 143.4173 Evaluate side-chains 90 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain D residue 136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 34 optimal weight: 0.0980 chunk 86 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN D 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.089418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.079740 restraints weight = 15466.731| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 1.31 r_work: 0.2655 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12254 Z= 0.136 Angle : 0.528 5.678 16668 Z= 0.283 Chirality : 0.047 0.160 1736 Planarity : 0.004 0.043 2168 Dihedral : 4.660 19.542 1652 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.98 % Allowed : 7.45 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % 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: -1.04 (0.21), residues: 1532 helix: -2.95 (0.74), residues: 24 sheet: 0.48 (0.22), residues: 568 loop : -1.45 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 89 HIS 0.004 0.001 HIS D 207 PHE 0.016 0.002 PHE C 316 TYR 0.008 0.001 TYR B 163 ARG 0.002 0.000 ARG D 203 Details of bonding type rmsd hydrogen bonds : bond 0.03181 ( 360) hydrogen bonds : angle 6.32413 ( 975) SS BOND : bond 0.00233 ( 22) SS BOND : angle 0.80191 ( 44) covalent geometry : bond 0.00341 (12232) covalent geometry : angle 0.52675 (16624) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 1.540 Fit side-chains revert: symmetry clash REVERT: A 46 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7627 (mm-40) REVERT: C 249 SER cc_start: 0.7968 (t) cc_final: 0.7682 (m) outliers start: 13 outliers final: 6 residues processed: 96 average time/residue: 1.3046 time to fit residues: 136.6216 Evaluate side-chains 85 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 129 TRP Chi-restraints excluded: chain D residue 267 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 79 optimal weight: 0.0070 chunk 142 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.089221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.079638 restraints weight = 15216.211| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 1.30 r_work: 0.2637 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12254 Z= 0.136 Angle : 0.520 5.640 16668 Z= 0.279 Chirality : 0.047 0.160 1736 Planarity : 0.004 0.042 2168 Dihedral : 4.653 19.409 1652 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.58 % Allowed : 8.73 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % 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 (0.21), residues: 1532 helix: -3.01 (0.72), residues: 24 sheet: 0.51 (0.22), residues: 568 loop : -1.42 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 89 HIS 0.005 0.001 HIS A 207 PHE 0.015 0.002 PHE C 316 TYR 0.007 0.001 TYR B 163 ARG 0.002 0.000 ARG C 28 Details of bonding type rmsd hydrogen bonds : bond 0.03004 ( 360) hydrogen bonds : angle 6.14373 ( 975) SS BOND : bond 0.00234 ( 22) SS BOND : angle 0.66639 ( 44) covalent geometry : bond 0.00343 (12232) covalent geometry : angle 0.51980 (16624) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 1.360 Fit side-chains revert: symmetry clash REVERT: A 46 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7639 (mm-40) REVERT: A 81 ASN cc_start: 0.9188 (OUTLIER) cc_final: 0.8753 (p0) REVERT: B 46 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7985 (mt0) REVERT: C 46 GLN cc_start: 0.7719 (mm-40) cc_final: 0.7436 (mm-40) REVERT: C 302 ASP cc_start: 0.8848 (m-30) cc_final: 0.8568 (m-30) REVERT: D 46 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7941 (mt0) outliers start: 21 outliers final: 12 residues processed: 99 average time/residue: 1.2421 time to fit residues: 135.3203 Evaluate side-chains 97 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 129 TRP Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 317 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 108 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 235 ASN D 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.087109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.077603 restraints weight = 15381.545| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 1.31 r_work: 0.2619 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2509 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12254 Z= 0.195 Angle : 0.559 5.760 16668 Z= 0.299 Chirality : 0.048 0.161 1736 Planarity : 0.004 0.043 2168 Dihedral : 4.850 20.041 1652 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.73 % Allowed : 10.02 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % 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: -1.09 (0.21), residues: 1532 helix: -3.19 (0.68), residues: 24 sheet: 0.39 (0.22), residues: 588 loop : -1.48 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 89 HIS 0.007 0.001 HIS D 207 PHE 0.017 0.002 PHE D 31 TYR 0.008 0.001 TYR C 163 ARG 0.003 0.000 ARG D 203 Details of bonding type rmsd hydrogen bonds : bond 0.03253 ( 360) hydrogen bonds : angle 6.19253 ( 975) SS BOND : bond 0.00296 ( 22) SS BOND : angle 0.71438 ( 44) covalent geometry : bond 0.00497 (12232) covalent geometry : angle 0.55896 (16624) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 1.322 Fit side-chains revert: symmetry clash REVERT: A 46 GLN cc_start: 0.8080 (mm-40) cc_final: 0.7701 (mm-40) REVERT: A 81 ASN cc_start: 0.9113 (OUTLIER) cc_final: 0.8840 (p0) REVERT: B 46 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8036 (mt0) REVERT: C 46 GLN cc_start: 0.7806 (mm-40) cc_final: 0.7400 (mm-40) REVERT: D 46 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7980 (mt0) REVERT: D 342 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.5989 (mt-10) outliers start: 23 outliers final: 15 residues processed: 99 average time/residue: 1.1073 time to fit residues: 120.9738 Evaluate side-chains 97 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 129 TRP Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 342 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 118 optimal weight: 0.0060 chunk 57 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN D 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.088802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.079438 restraints weight = 15487.646| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 1.27 r_work: 0.2640 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12254 Z= 0.127 Angle : 0.517 5.418 16668 Z= 0.278 Chirality : 0.046 0.159 1736 Planarity : 0.004 0.042 2168 Dihedral : 4.712 19.612 1652 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.81 % Allowed : 11.14 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % 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: -1.08 (0.21), residues: 1532 helix: None (None), residues: 0 sheet: 0.42 (0.23), residues: 544 loop : -1.47 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 89 HIS 0.004 0.001 HIS D 207 PHE 0.015 0.002 PHE D 31 TYR 0.007 0.001 TYR C 163 ARG 0.002 0.000 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.02913 ( 360) hydrogen bonds : angle 6.05140 ( 975) SS BOND : bond 0.00228 ( 22) SS BOND : angle 0.52356 ( 44) covalent geometry : bond 0.00319 (12232) covalent geometry : angle 0.51709 (16624) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 1.307 Fit side-chains revert: symmetry clash REVERT: A 46 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7703 (mm-40) REVERT: A 129 TRP cc_start: 0.6938 (OUTLIER) cc_final: 0.6582 (p90) REVERT: B 46 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7971 (mt0) REVERT: C 46 GLN cc_start: 0.7831 (mm-40) cc_final: 0.7454 (mm-40) REVERT: D 46 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7838 (mt0) outliers start: 24 outliers final: 15 residues processed: 97 average time/residue: 1.2294 time to fit residues: 130.6641 Evaluate side-chains 96 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 129 TRP Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 317 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 77 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.087305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.078004 restraints weight = 15443.629| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 1.26 r_work: 0.2612 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2504 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12254 Z= 0.185 Angle : 0.551 5.620 16668 Z= 0.295 Chirality : 0.048 0.160 1736 Planarity : 0.004 0.042 2168 Dihedral : 4.874 20.242 1652 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.81 % Allowed : 11.60 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % 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: -1.11 (0.21), residues: 1532 helix: None (None), residues: 0 sheet: 0.40 (0.22), residues: 588 loop : -1.57 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 89 HIS 0.006 0.001 HIS D 207 PHE 0.017 0.002 PHE D 31 TYR 0.007 0.001 TYR C 163 ARG 0.003 0.000 ARG C 203 Details of bonding type rmsd hydrogen bonds : bond 0.03166 ( 360) hydrogen bonds : angle 6.12876 ( 975) SS BOND : bond 0.00289 ( 22) SS BOND : angle 0.67122 ( 44) covalent geometry : bond 0.00469 (12232) covalent geometry : angle 0.55103 (16624) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 1.307 Fit side-chains revert: symmetry clash REVERT: A 46 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7722 (mm-40) REVERT: B 46 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8011 (mt0) REVERT: C 46 GLN cc_start: 0.7842 (mm-40) cc_final: 0.7481 (mm-40) REVERT: D 46 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7841 (mt0) outliers start: 24 outliers final: 18 residues processed: 96 average time/residue: 1.1913 time to fit residues: 125.6262 Evaluate side-chains 97 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 129 TRP Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 317 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 4.9990 chunk 62 optimal weight: 0.3980 chunk 136 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN D 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.088199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.078626 restraints weight = 15447.872| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 1.32 r_work: 0.2624 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12254 Z= 0.142 Angle : 0.523 5.457 16668 Z= 0.281 Chirality : 0.047 0.161 1736 Planarity : 0.004 0.042 2168 Dihedral : 4.750 19.972 1652 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.96 % Allowed : 11.67 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % 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: -1.09 (0.21), residues: 1532 helix: None (None), residues: 0 sheet: 0.43 (0.23), residues: 544 loop : -1.49 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 89 HIS 0.005 0.001 HIS D 207 PHE 0.015 0.002 PHE D 31 TYR 0.007 0.001 TYR C 163 ARG 0.002 0.000 ARG C 28 Details of bonding type rmsd hydrogen bonds : bond 0.02960 ( 360) hydrogen bonds : angle 6.03682 ( 975) SS BOND : bond 0.00243 ( 22) SS BOND : angle 0.53594 ( 44) covalent geometry : bond 0.00358 (12232) covalent geometry : angle 0.52281 (16624) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 1.310 Fit side-chains revert: symmetry clash REVERT: A 46 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7709 (mm-40) REVERT: A 129 TRP cc_start: 0.7234 (OUTLIER) cc_final: 0.6658 (p90) REVERT: B 46 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.8004 (mt0) REVERT: C 46 GLN cc_start: 0.7835 (mm-40) cc_final: 0.7470 (mm-40) REVERT: C 83 ARG cc_start: 0.8165 (ttm170) cc_final: 0.7811 (ttm170) REVERT: D 46 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7835 (mt0) REVERT: D 342 GLU cc_start: 0.6648 (OUTLIER) cc_final: 0.5967 (mp0) outliers start: 26 outliers final: 18 residues processed: 96 average time/residue: 1.2266 time to fit residues: 128.9482 Evaluate side-chains 99 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 129 TRP Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 342 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 101 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 120 optimal weight: 0.0970 chunk 117 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 124 optimal weight: 0.0470 chunk 122 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN D 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.089714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.080424 restraints weight = 15371.658| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 1.25 r_work: 0.2651 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12254 Z= 0.119 Angle : 0.502 5.407 16668 Z= 0.269 Chirality : 0.046 0.163 1736 Planarity : 0.004 0.042 2168 Dihedral : 4.590 18.641 1652 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.03 % Allowed : 11.67 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.95 % 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: -0.93 (0.22), residues: 1532 helix: None (None), residues: 0 sheet: 0.56 (0.22), residues: 568 loop : -1.44 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 89 HIS 0.003 0.001 HIS D 207 PHE 0.014 0.001 PHE C 316 TYR 0.008 0.001 TYR C 163 ARG 0.001 0.000 ARG C 28 Details of bonding type rmsd hydrogen bonds : bond 0.02764 ( 360) hydrogen bonds : angle 5.91316 ( 975) SS BOND : bond 0.00208 ( 22) SS BOND : angle 0.46087 ( 44) covalent geometry : bond 0.00297 (12232) covalent geometry : angle 0.50182 (16624) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 1.367 Fit side-chains revert: symmetry clash REVERT: A 46 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7675 (mm-40) REVERT: A 129 TRP cc_start: 0.7205 (OUTLIER) cc_final: 0.6686 (p90) REVERT: B 81 ASN cc_start: 0.9217 (OUTLIER) cc_final: 0.8961 (p0) REVERT: C 46 GLN cc_start: 0.7818 (mm-40) cc_final: 0.7455 (mm-40) REVERT: C 83 ARG cc_start: 0.8157 (ttm170) cc_final: 0.7816 (ttm170) REVERT: D 46 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7803 (mt0) REVERT: D 152 MET cc_start: 0.9131 (mtt) cc_final: 0.8920 (mtt) REVERT: D 342 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.5955 (mp0) outliers start: 27 outliers final: 18 residues processed: 93 average time/residue: 1.2296 time to fit residues: 125.4418 Evaluate side-chains 95 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 129 TRP Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 342 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 96 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 70 optimal weight: 0.1980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.090051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.080782 restraints weight = 15261.847| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 1.24 r_work: 0.2654 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 12254 Z= 0.174 Angle : 0.779 59.130 16668 Z= 0.462 Chirality : 0.048 0.581 1736 Planarity : 0.004 0.042 2168 Dihedral : 4.614 19.564 1652 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.96 % Allowed : 11.75 % Favored : 86.30 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.95 % 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: -0.93 (0.22), residues: 1532 helix: None (None), residues: 0 sheet: 0.56 (0.22), residues: 568 loop : -1.44 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 89 HIS 0.003 0.001 HIS D 207 PHE 0.014 0.001 PHE C 316 TYR 0.008 0.001 TYR B 80 ARG 0.001 0.000 ARG C 28 Details of bonding type rmsd hydrogen bonds : bond 0.02771 ( 360) hydrogen bonds : angle 5.91458 ( 975) SS BOND : bond 0.00212 ( 22) SS BOND : angle 0.46622 ( 44) covalent geometry : bond 0.00383 (12232) covalent geometry : angle 0.77939 (16624) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 1.297 Fit side-chains revert: symmetry clash REVERT: A 46 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7680 (mm-40) REVERT: A 129 TRP cc_start: 0.7216 (OUTLIER) cc_final: 0.6698 (p90) REVERT: C 46 GLN cc_start: 0.7825 (mm-40) cc_final: 0.7464 (mm-40) REVERT: C 83 ARG cc_start: 0.8163 (ttm170) cc_final: 0.7822 (ttm170) REVERT: D 46 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7807 (mt0) REVERT: D 342 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.5964 (mp0) outliers start: 26 outliers final: 20 residues processed: 91 average time/residue: 1.1841 time to fit residues: 118.1018 Evaluate side-chains 97 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 129 TRP Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 172 LYS Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 342 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 7 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 140 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.089702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.080115 restraints weight = 15213.564| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 1.31 r_work: 0.2665 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 12254 Z= 0.164 Angle : 0.768 59.195 16668 Z= 0.447 Chirality : 0.046 0.162 1736 Planarity : 0.004 0.042 2168 Dihedral : 4.603 18.611 1652 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.81 % Allowed : 11.82 % Favored : 86.37 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.95 % 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: -0.93 (0.22), residues: 1532 helix: None (None), residues: 0 sheet: 0.56 (0.22), residues: 568 loop : -1.44 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 89 HIS 0.003 0.001 HIS D 207 PHE 0.014 0.001 PHE C 316 TYR 0.007 0.001 TYR C 163 ARG 0.001 0.000 ARG A 203 Details of bonding type rmsd hydrogen bonds : bond 0.02778 ( 360) hydrogen bonds : angle 5.91486 ( 975) SS BOND : bond 0.00211 ( 22) SS BOND : angle 0.46883 ( 44) covalent geometry : bond 0.00368 (12232) covalent geometry : angle 0.76887 (16624) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5831.96 seconds wall clock time: 102 minutes 1.52 seconds (6121.52 seconds total)