Starting phenix.real_space_refine on Tue Jun 10 14:58:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ewq_50022/06_2025/9ewq_50022.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ewq_50022/06_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_50022/06_2025/9ewq_50022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ewq_50022/06_2025/9ewq_50022.map" model { file = "/net/cci-nas-00/data/ceres_data/9ewq_50022/06_2025/9ewq_50022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ewq_50022/06_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 7.34, per 1000 atoms: 0.62 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: 2.41 Conformation dependent library (CDL) restraints added in 1.5 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: 1.39 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: 3.58 Time building geometry restraints manager: 2.95 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: 3.560 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 27.960 Find NCS groups from input model: 0.380 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:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.950 ------------------------------------------------------------------------------- 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 : 1.446 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 100 average time/residue: 1.3532 time to fit residues: 147.4812 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 : 1.256 ------------------------------------------------------------------------------- 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 = 34)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.079420 restraints weight = 15330.948| |-----------------------------------------------------------------------------| 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: 0.8512 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 : 1.302 Fit side-chains revert: symmetry clash REVERT: C 46 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7309 (mt0) REVERT: C 249 SER cc_start: 0.8008 (t) cc_final: 0.7744 (m) REVERT: C 302 ASP cc_start: 0.8829 (m-30) cc_final: 0.8539 (m-30) outliers start: 9 outliers final: 2 residues processed: 98 average time/residue: 1.4612 time to fit residues: 156.6450 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 : 2.030 ------------------------------------------------------------------------------- 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: 0.9990 chunk 42 optimal weight: 0.0980 chunk 116 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.2863 r_free = 0.2863 target = 0.089128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.079687 restraints weight = 15462.017| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 1.27 r_work: 0.2645 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2537 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12254 Z= 0.143 Angle : 0.533 5.704 16668 Z= 0.286 Chirality : 0.047 0.161 1736 Planarity : 0.004 0.043 2168 Dihedral : 4.692 19.767 1652 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.98 % Allowed : 7.38 % Favored : 91.64 % 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: -1.06 (0.21), residues: 1532 helix: -2.97 (0.74), residues: 24 sheet: 0.47 (0.22), residues: 568 loop : -1.47 (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 0.017 0.002 PHE C 316 TYR 0.008 0.001 TYR B 163 ARG 0.003 0.000 ARG D 203 Details of bonding type rmsd hydrogen bonds : bond 0.03229 ( 360) hydrogen bonds : angle 6.35732 ( 975) SS BOND : bond 0.00249 ( 22) SS BOND : angle 0.81097 ( 44) covalent geometry : bond 0.00359 (12232) covalent geometry : angle 0.53237 (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 99 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 1.999 Fit side-chains revert: symmetry clash REVERT: A 46 GLN cc_start: 0.7990 (mm-40) cc_final: 0.7618 (mm-40) REVERT: D 342 GLU cc_start: 0.6639 (OUTLIER) cc_final: 0.6031 (mt-10) outliers start: 13 outliers final: 6 residues processed: 92 average time/residue: 1.2632 time to fit residues: 127.8644 Evaluate side-chains 87 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 1.419 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 342 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 79 optimal weight: 0.5980 chunk 142 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 105 optimal weight: 0.4980 chunk 103 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.2839 r_free = 0.2839 target = 0.087801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.078521 restraints weight = 15346.283| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 1.25 r_work: 0.2634 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12254 Z= 0.167 Angle : 0.545 5.710 16668 Z= 0.292 Chirality : 0.048 0.160 1736 Planarity : 0.004 0.043 2168 Dihedral : 4.795 20.154 1652 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.73 % Allowed : 8.51 % Favored : 89.76 % 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: -3.10 (0.71), residues: 24 sheet: 0.46 (0.22), residues: 568 loop : -1.48 (0.20), residues: 940 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 0.016 0.002 PHE B 316 TYR 0.007 0.001 TYR B 163 ARG 0.003 0.000 ARG D 203 Details of bonding type rmsd hydrogen bonds : bond 0.03198 ( 360) hydrogen bonds : angle 6.23969 ( 975) SS BOND : bond 0.00283 ( 22) SS BOND : angle 0.71817 ( 44) covalent geometry : bond 0.00421 (12232) covalent geometry : angle 0.54416 (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 110 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 1.436 Fit side-chains revert: symmetry clash REVERT: A 46 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7694 (mm-40) REVERT: B 46 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7987 (mt0) REVERT: C 46 GLN cc_start: 0.7756 (mm-40) cc_final: 0.7511 (mm-40) outliers start: 23 outliers final: 12 residues processed: 102 average time/residue: 1.1317 time to fit residues: 127.6693 Evaluate side-chains 95 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 1.443 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 100 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 73 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 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 = 0.2852 r_free = 0.2852 target = 0.088464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.079212 restraints weight = 15306.625| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 1.24 r_work: 0.2633 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12254 Z= 0.147 Angle : 0.528 5.584 16668 Z= 0.284 Chirality : 0.047 0.160 1736 Planarity : 0.004 0.042 2168 Dihedral : 4.750 19.839 1652 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.51 % Allowed : 10.47 % Favored : 88.03 % 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: -1.03 (0.21), residues: 1532 helix: None (None), residues: 0 sheet: 0.50 (0.22), residues: 568 loop : -1.52 (0.19), residues: 964 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 0.03041 ( 360) hydrogen bonds : angle 6.11748 ( 975) SS BOND : bond 0.00252 ( 22) SS BOND : angle 0.60229 ( 44) covalent geometry : bond 0.00372 (12232) covalent geometry : angle 0.52826 (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 104 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 1.208 Fit side-chains revert: symmetry clash REVERT: A 46 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7684 (mm-40) REVERT: B 46 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8020 (mt0) REVERT: C 46 GLN cc_start: 0.7784 (mm-40) cc_final: 0.7487 (mm-40) outliers start: 20 outliers final: 17 residues processed: 97 average time/residue: 1.3173 time to fit residues: 140.3581 Evaluate side-chains 97 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 1.277 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.2794 r_free = 0.2794 target = 0.084801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.075040 restraints weight = 15744.127| |-----------------------------------------------------------------------------| r_work (start): 0.2638 rms_B_bonded: 1.37 r_work: 0.2564 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2452 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 12254 Z= 0.278 Angle : 0.625 5.809 16668 Z= 0.334 Chirality : 0.051 0.157 1736 Planarity : 0.005 0.044 2168 Dihedral : 5.203 21.915 1652 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 1.81 % Allowed : 11.52 % Favored : 86.67 % 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: -3.54 (0.57), residues: 24 sheet: 0.38 (0.22), residues: 560 loop : -1.71 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 89 HIS 0.011 0.002 HIS B 207 PHE 0.021 0.002 PHE D 31 TYR 0.008 0.001 TYR B 163 ARG 0.004 0.001 ARG C 203 Details of bonding type rmsd hydrogen bonds : bond 0.03649 ( 360) hydrogen bonds : angle 6.37753 ( 975) SS BOND : bond 0.00386 ( 22) SS BOND : angle 0.92012 ( 44) covalent geometry : bond 0.00704 (12232) covalent geometry : angle 0.62354 (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 102 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 1.343 Fit side-chains revert: symmetry clash REVERT: A 46 GLN cc_start: 0.7916 (mm-40) cc_final: 0.7545 (mm-40) REVERT: B 46 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8027 (mt0) REVERT: C 46 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7540 (mm-40) outliers start: 24 outliers final: 15 residues processed: 91 average time/residue: 1.5303 time to fit residues: 152.0231 Evaluate side-chains 93 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 1.273 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 77 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.2838 r_free = 0.2838 target = 0.087530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.078296 restraints weight = 15429.422| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 1.25 r_work: 0.2614 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1033 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= 0.155 Angle : 0.540 5.435 16668 Z= 0.290 Chirality : 0.047 0.161 1736 Planarity : 0.004 0.046 2168 Dihedral : 4.914 21.219 1652 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.81 % Allowed : 12.05 % Favored : 86.14 % 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: -1.26 (0.21), residues: 1532 helix: None (None), residues: 0 sheet: 0.26 (0.22), residues: 564 loop : -1.61 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 89 HIS 0.005 0.001 HIS A 207 PHE 0.016 0.002 PHE C 316 TYR 0.007 0.001 TYR C 163 ARG 0.002 0.000 ARG C 28 Details of bonding type rmsd hydrogen bonds : bond 0.03062 ( 360) hydrogen bonds : angle 6.15723 ( 975) SS BOND : bond 0.00257 ( 22) SS BOND : angle 0.56505 ( 44) covalent geometry : bond 0.00390 (12232) covalent geometry : angle 0.53993 (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 106 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 1.621 Fit side-chains revert: symmetry clash REVERT: A 46 GLN cc_start: 0.8115 (mm-40) cc_final: 0.7748 (mm-40) REVERT: B 46 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8014 (mt0) REVERT: C 46 GLN cc_start: 0.7835 (mm-40) cc_final: 0.7537 (mm-40) REVERT: C 83 ARG cc_start: 0.8145 (ttm170) cc_final: 0.7802 (ttm170) outliers start: 24 outliers final: 17 residues processed: 98 average time/residue: 1.6367 time to fit residues: 177.4103 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 : 1.459 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 136 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 135 optimal weight: 0.3980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.2836 r_free = 0.2836 target = 0.087598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.078059 restraints weight = 15486.469| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 1.31 r_work: 0.2626 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12254 Z= 0.149 Angle : 0.532 5.509 16668 Z= 0.285 Chirality : 0.047 0.161 1736 Planarity : 0.004 0.045 2168 Dihedral : 4.841 20.456 1652 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % 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: -1.20 (0.21), residues: 1532 helix: None (None), residues: 0 sheet: 0.37 (0.23), residues: 544 loop : -1.58 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 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 135 Details of bonding type rmsd hydrogen bonds : bond 0.02987 ( 360) hydrogen bonds : angle 6.08371 ( 975) SS BOND : bond 0.00252 ( 22) SS BOND : angle 0.55443 ( 44) covalent geometry : bond 0.00376 (12232) covalent geometry : angle 0.53205 (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 108 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 1.451 Fit side-chains revert: symmetry clash REVERT: A 46 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7706 (mm-40) REVERT: B 46 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8013 (mt0) REVERT: C 46 GLN cc_start: 0.7851 (mm-40) cc_final: 0.7571 (mm-40) REVERT: C 83 ARG cc_start: 0.8161 (ttm170) cc_final: 0.7796 (ttm170) REVERT: D 9 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8593 (tp) outliers start: 27 outliers final: 21 residues processed: 99 average time/residue: 1.5712 time to fit residues: 171.9590 Evaluate side-chains 100 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 37 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 9 ILE 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 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: 0.8980 chunk 120 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 122 optimal weight: 0.0980 chunk 47 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.2838 r_free = 0.2838 target = 0.087763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.078242 restraints weight = 15452.270| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 1.31 r_work: 0.2620 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2510 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12254 Z= 0.146 Angle : 0.529 5.479 16668 Z= 0.284 Chirality : 0.047 0.161 1736 Planarity : 0.004 0.045 2168 Dihedral : 4.812 20.278 1652 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.03 % Allowed : 11.82 % Favored : 86.14 % 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: -1.15 (0.21), residues: 1532 helix: None (None), residues: 0 sheet: 0.41 (0.23), residues: 544 loop : -1.55 (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 0.003 0.000 ARG C 203 Details of bonding type rmsd hydrogen bonds : bond 0.02953 ( 360) hydrogen bonds : angle 6.05297 ( 975) SS BOND : bond 0.00245 ( 22) SS BOND : angle 0.54454 ( 44) covalent geometry : bond 0.00368 (12232) covalent geometry : angle 0.52882 (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 107 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 1.360 Fit side-chains revert: symmetry clash REVERT: A 46 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7704 (mm-40) REVERT: B 46 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.8004 (mt0) REVERT: C 46 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7601 (mm-40) REVERT: C 83 ARG cc_start: 0.8164 (ttm170) cc_final: 0.7807 (ttm170) REVERT: D 9 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8601 (tp) outliers start: 27 outliers final: 22 residues processed: 98 average time/residue: 1.1727 time to fit residues: 126.5843 Evaluate side-chains 102 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 37 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 C residue 325 LEU Chi-restraints excluded: chain D residue 9 ILE 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 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: 0.8980 chunk 2 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.2835 r_free = 0.2835 target = 0.087618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.078113 restraints weight = 15391.757| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 1.30 r_work: 0.2622 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1103 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= 0.156 Angle : 0.534 5.548 16668 Z= 0.286 Chirality : 0.047 0.160 1736 Planarity : 0.004 0.045 2168 Dihedral : 4.832 20.271 1652 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % 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: -1.15 (0.21), residues: 1532 helix: None (None), residues: 0 sheet: 0.41 (0.23), residues: 544 loop : -1.55 (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 B 207 PHE 0.015 0.002 PHE D 31 TYR 0.007 0.001 TYR C 163 ARG 0.002 0.000 ARG C 203 Details of bonding type rmsd hydrogen bonds : bond 0.02962 ( 360) hydrogen bonds : angle 6.05573 ( 975) SS BOND : bond 0.00253 ( 22) SS BOND : angle 0.57234 ( 44) covalent geometry : bond 0.00394 (12232) covalent geometry : angle 0.53419 (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 105 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 1.704 Fit side-chains revert: symmetry clash REVERT: A 46 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7702 (mm-40) REVERT: B 46 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.8014 (mt0) REVERT: C 46 GLN cc_start: 0.7875 (mm-40) cc_final: 0.7602 (mm-40) REVERT: C 83 ARG cc_start: 0.8158 (ttm170) cc_final: 0.7797 (ttm170) REVERT: D 9 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8603 (tp) outliers start: 27 outliers final: 21 residues processed: 95 average time/residue: 1.1449 time to fit residues: 120.0694 Evaluate side-chains 101 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 129 TRP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 37 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 274 SER Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain D residue 9 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 7 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 142 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 57 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.2851 r_free = 0.2851 target = 0.088359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.079151 restraints weight = 15239.445| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 1.24 r_work: 0.2632 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12254 Z= 0.139 Angle : 0.522 5.470 16668 Z= 0.280 Chirality : 0.047 0.161 1736 Planarity : 0.004 0.044 2168 Dihedral : 4.762 19.939 1652 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.03 % Allowed : 11.82 % Favored : 86.14 % 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: 0.43 (0.23), residues: 544 loop : -1.51 (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 203 Details of bonding type rmsd hydrogen bonds : bond 0.02887 ( 360) hydrogen bonds : angle 5.99658 ( 975) SS BOND : bond 0.00239 ( 22) SS BOND : angle 0.52145 ( 44) covalent geometry : bond 0.00350 (12232) covalent geometry : angle 0.52187 (16624) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6332.96 seconds wall clock time: 114 minutes 1.37 seconds (6841.37 seconds total)