Starting phenix.real_space_refine on Tue Mar 3 21:24:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xk2_33241/03_2026/7xk2_33241.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xk2_33241/03_2026/7xk2_33241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xk2_33241/03_2026/7xk2_33241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xk2_33241/03_2026/7xk2_33241.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xk2_33241/03_2026/7xk2_33241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xk2_33241/03_2026/7xk2_33241.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.001 sd= 0.085 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 66 5.16 5 C 5594 2.51 5 N 1509 2.21 5 O 1622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8791 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1798 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Chain: "B" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2596 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 2229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2229 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 9, 'TRANS': 274} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "S" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1711 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 429 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'FI7': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.89, per 1000 atoms: 0.21 Number of scatterers: 8791 At special positions: 0 Unit cell: (87.36, 116.48, 132.08, 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 66 16.00 O 1622 8.00 N 1509 7.00 C 5594 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " distance=2.03 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: 0.47 Conformation dependent library (CDL) restraints added in 304.2 milliseconds 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 15 sheets defined 34.9% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.608A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 removed outlier: 3.650A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.747A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 273 through 281 Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.715A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'R' and resid 25 through 53 Proline residue: R 31 - end of helix removed outlier: 3.966A pdb=" N LEU R 43 " --> pdb=" O ILE R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 80 removed outlier: 3.894A pdb=" N PHE R 65 " --> pdb=" O SER R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 86 Processing helix chain 'R' and resid 97 through 130 removed outlier: 3.996A pdb=" N ARG R 101 " --> pdb=" O ASP R 97 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU R 104 " --> pdb=" O CYS R 100 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE R 105 " --> pdb=" O ARG R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 158 removed outlier: 3.650A pdb=" N LEU R 158 " --> pdb=" O ILE R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 165 removed outlier: 3.935A pdb=" N LYS R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS R 165 " --> pdb=" O HIS R 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 160 through 165' Processing helix chain 'R' and resid 188 through 218 removed outlier: 3.560A pdb=" N MET R 192 " --> pdb=" O TRP R 188 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) Proline residue: R 200 - end of helix removed outlier: 3.589A pdb=" N LEU R 205 " --> pdb=" O LEU R 201 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA R 209 " --> pdb=" O LEU R 205 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG R 210 " --> pdb=" O PHE R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 261 removed outlier: 3.843A pdb=" N ILE R 233 " --> pdb=" O ALA R 229 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET R 234 " --> pdb=" O ILE R 230 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 271 through 290 Processing helix chain 'R' and resid 291 through 294 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 74 through 76 No H-bonds generated for 'chain 'S' and resid 74 through 76' Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.614A pdb=" N ASP S 223 " --> pdb=" O GLU S 220 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 220 through 224' Processing helix chain 'C' and resid 8 through 24 removed outlier: 4.198A pdb=" N ALA C 12 " --> pdb=" O SER C 8 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.814A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 187 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 187 removed outlier: 7.133A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.266A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.749A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.007A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.954A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 189 through 192 removed outlier: 6.630A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.836A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.620A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 6 through 7 removed outlier: 3.728A pdb=" N SER S 7 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 Processing sheet with id=AB3, first strand: chain 'S' and resid 38 through 39 Processing sheet with id=AB4, first strand: chain 'S' and resid 92 through 93 Processing sheet with id=AB5, first strand: chain 'S' and resid 156 through 159 removed outlier: 3.748A pdb=" N THR S 215 " --> pdb=" O SER S 204 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER S 204 " --> pdb=" O THR S 215 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 186 through 189 removed outlier: 6.623A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 393 hydrogen bonds defined for protein. 1104 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: 1.12 Time building geometry restraints manager: 0.72 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: 2528 1.34 - 1.46: 1693 1.46 - 1.57: 4662 1.57 - 1.69: 2 1.69 - 1.81: 96 Bond restraints: 8981 Sorted by residual: bond pdb=" C02 FI7 R 401 " pdb=" C17 FI7 R 401 " ideal model delta sigma weight residual 1.545 1.627 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C17 FI7 R 401 " pdb=" N19 FI7 R 401 " ideal model delta sigma weight residual 1.348 1.414 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" C07 FI7 R 401 " pdb=" N15 FI7 R 401 " ideal model delta sigma weight residual 1.300 1.365 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C02 FI7 R 401 " pdb=" C04 FI7 R 401 " ideal model delta sigma weight residual 1.546 1.606 -0.060 2.00e-02 2.50e+03 9.14e+00 bond pdb=" C05 FI7 R 401 " pdb=" O16 FI7 R 401 " ideal model delta sigma weight residual 1.330 1.390 -0.060 2.00e-02 2.50e+03 8.96e+00 ... (remaining 8976 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 11871 2.76 - 5.52: 220 5.52 - 8.28: 46 8.28 - 11.04: 15 11.04 - 13.80: 9 Bond angle restraints: 12161 Sorted by residual: angle pdb=" CA GLN A 52 " pdb=" CB GLN A 52 " pdb=" CG GLN A 52 " ideal model delta sigma weight residual 114.10 124.36 -10.26 2.00e+00 2.50e-01 2.63e+01 angle pdb=" C ALA R 174 " pdb=" N ASN R 175 " pdb=" CA ASN R 175 " ideal model delta sigma weight residual 122.46 129.13 -6.67 1.41e+00 5.03e-01 2.23e+01 angle pdb=" CA LYS C 20 " pdb=" CB LYS C 20 " pdb=" CG LYS C 20 " ideal model delta sigma weight residual 114.10 123.43 -9.33 2.00e+00 2.50e-01 2.18e+01 angle pdb=" C THR R 283 " pdb=" N TYR R 284 " pdb=" CA TYR R 284 " ideal model delta sigma weight residual 121.58 112.72 8.86 1.95e+00 2.63e-01 2.07e+01 angle pdb=" CA TYR R 284 " pdb=" CB TYR R 284 " pdb=" CG TYR R 284 " ideal model delta sigma weight residual 113.90 121.60 -7.70 1.80e+00 3.09e-01 1.83e+01 ... (remaining 12156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 4590 17.63 - 35.25: 579 35.25 - 52.88: 133 52.88 - 70.51: 20 70.51 - 88.14: 7 Dihedral angle restraints: 5329 sinusoidal: 2063 harmonic: 3266 Sorted by residual: dihedral pdb=" CB CYS R 19 " pdb=" SG CYS R 19 " pdb=" SG CYS R 266 " pdb=" CB CYS R 266 " ideal model delta sinusoidal sigma weight residual 93.00 160.11 -67.11 1 1.00e+01 1.00e-02 5.87e+01 dihedral pdb=" CB CYS R 18 " pdb=" SG CYS R 18 " pdb=" SG CYS R 183 " pdb=" CB CYS R 183 " ideal model delta sinusoidal sigma weight residual -86.00 -35.39 -50.61 1 1.00e+01 1.00e-02 3.51e+01 dihedral pdb=" CA TYR S 94 " pdb=" C TYR S 94 " pdb=" N TYR S 95 " pdb=" CA TYR S 95 " ideal model delta harmonic sigma weight residual 180.00 151.95 28.05 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 5326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1255 0.100 - 0.199: 99 0.199 - 0.298: 8 0.298 - 0.398: 1 0.398 - 0.497: 1 Chirality restraints: 1364 Sorted by residual: chirality pdb=" CB ILE R 238 " pdb=" CA ILE R 238 " pdb=" CG1 ILE R 238 " pdb=" CG2 ILE R 238 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.19e+00 chirality pdb=" CG LEU R 80 " pdb=" CB LEU R 80 " pdb=" CD1 LEU R 80 " pdb=" CD2 LEU R 80 " both_signs ideal model delta sigma weight residual False -2.59 -2.91 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA TYR R 284 " pdb=" N TYR R 284 " pdb=" C TYR R 284 " pdb=" CB TYR R 284 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1361 not shown) Planarity restraints: 1542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 265 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.12e+00 pdb=" C ILE A 265 " -0.049 2.00e-02 2.50e+03 pdb=" O ILE A 265 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU A 266 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 134 " 0.191 9.50e-02 1.11e+02 8.64e-02 5.90e+00 pdb=" NE ARG B 134 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 134 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG B 134 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 134 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 197 " -0.181 9.50e-02 1.11e+02 8.18e-02 5.17e+00 pdb=" NE ARG B 197 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG B 197 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG B 197 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 197 " -0.001 2.00e-02 2.50e+03 ... (remaining 1539 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1903 2.78 - 3.31: 7739 3.31 - 3.84: 14840 3.84 - 4.37: 17084 4.37 - 4.90: 29646 Nonbonded interactions: 71212 Sorted by model distance: nonbonded pdb=" O ILE R 278 " pdb=" OG SER R 281 " model vdw 2.251 3.040 nonbonded pdb=" OD2 ASP B 83 " pdb=" OG1 THR B 86 " model vdw 2.291 3.040 nonbonded pdb=" OE1 GLN S 142 " pdb=" OG1 THR S 243 " model vdw 2.297 3.040 nonbonded pdb=" OG SER S 206 " pdb=" O THR S 213 " model vdw 2.313 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.329 3.040 ... (remaining 71207 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.220 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.770 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 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 : 0.005 0.082 8984 Z= 0.239 Angle : 1.022 13.801 12167 Z= 0.515 Chirality : 0.056 0.497 1364 Planarity : 0.007 0.086 1542 Dihedral : 16.480 88.136 3210 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.32 % Allowed : 22.03 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.23), residues: 1114 helix: -1.04 (0.25), residues: 355 sheet: -1.11 (0.30), residues: 265 loop : -2.24 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG S 160 TYR 0.035 0.002 TYR S 235 PHE 0.036 0.002 PHE A 334 TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS R 223 Details of bonding type rmsd covalent geometry : bond 0.00505 ( 8981) covalent geometry : angle 1.02170 (12161) SS BOND : bond 0.00115 ( 3) SS BOND : angle 0.90234 ( 6) hydrogen bonds : bond 0.14575 ( 379) hydrogen bonds : angle 6.75066 ( 1104) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 170 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: B 301 LYS cc_start: 0.7031 (ptmm) cc_final: 0.6631 (pttt) REVERT: S 80 PHE cc_start: 0.8645 (m-80) cc_final: 0.8348 (m-80) REVERT: C 18 GLN cc_start: 0.7912 (tp-100) cc_final: 0.7645 (tp-100) outliers start: 3 outliers final: 2 residues processed: 172 average time/residue: 0.1008 time to fit residues: 23.2101 Evaluate side-chains 169 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 167 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 280 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.0980 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 259 GLN R 110 ASN S 142 GLN C 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.189838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.128872 restraints weight = 10310.751| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.69 r_work: 0.3185 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8984 Z= 0.130 Angle : 0.628 8.613 12167 Z= 0.324 Chirality : 0.042 0.209 1364 Planarity : 0.005 0.047 1542 Dihedral : 5.657 42.679 1247 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.46 % Allowed : 21.71 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.24), residues: 1114 helix: 0.28 (0.27), residues: 359 sheet: -1.15 (0.30), residues: 274 loop : -2.05 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 160 TYR 0.028 0.001 TYR S 235 PHE 0.015 0.001 PHE A 196 TRP 0.015 0.001 TRP B 339 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8981) covalent geometry : angle 0.62791 (12161) SS BOND : bond 0.00099 ( 3) SS BOND : angle 0.75655 ( 6) hydrogen bonds : bond 0.03751 ( 379) hydrogen bonds : angle 4.87607 ( 1104) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 336 PHE cc_start: 0.8513 (t80) cc_final: 0.8306 (t80) REVERT: B 45 MET cc_start: 0.8379 (mtt) cc_final: 0.8153 (mtt) REVERT: B 301 LYS cc_start: 0.7106 (ptmm) cc_final: 0.6708 (pttt) REVERT: R 282 PHE cc_start: 0.8509 (m-80) cc_final: 0.8298 (m-80) REVERT: R 284 TYR cc_start: 0.7255 (OUTLIER) cc_final: 0.6962 (p90) REVERT: S 43 LYS cc_start: 0.8198 (mppt) cc_final: 0.7880 (mmtm) REVERT: S 180 ARG cc_start: 0.8492 (mtm-85) cc_final: 0.8149 (mtt90) REVERT: C 18 GLN cc_start: 0.7873 (tp40) cc_final: 0.7659 (tp-100) outliers start: 23 outliers final: 13 residues processed: 189 average time/residue: 0.1018 time to fit residues: 25.8642 Evaluate side-chains 178 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain C residue 37 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 67 optimal weight: 0.9990 chunk 59 optimal weight: 0.0980 chunk 107 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 102 optimal weight: 0.0050 chunk 25 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** S 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.188901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.123718 restraints weight = 10277.709| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.46 r_work: 0.3203 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8984 Z= 0.129 Angle : 0.611 11.273 12167 Z= 0.312 Chirality : 0.042 0.238 1364 Planarity : 0.004 0.044 1542 Dihedral : 5.241 38.418 1245 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.32 % Allowed : 21.50 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.25), residues: 1114 helix: 0.74 (0.28), residues: 366 sheet: -1.06 (0.30), residues: 274 loop : -1.89 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 134 TYR 0.030 0.001 TYR R 284 PHE 0.017 0.001 PHE R 276 TRP 0.011 0.001 TRP B 339 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8981) covalent geometry : angle 0.61090 (12161) SS BOND : bond 0.00077 ( 3) SS BOND : angle 0.74937 ( 6) hydrogen bonds : bond 0.03371 ( 379) hydrogen bonds : angle 4.57615 ( 1104) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7137 (tt0) REVERT: B 264 TYR cc_start: 0.9063 (m-80) cc_final: 0.8669 (m-80) REVERT: B 325 MET cc_start: 0.8083 (tpp) cc_final: 0.7858 (tpp) REVERT: R 194 LEU cc_start: 0.8569 (mm) cc_final: 0.7955 (tt) REVERT: R 227 LYS cc_start: 0.7944 (mmmm) cc_final: 0.7352 (mppt) REVERT: R 282 PHE cc_start: 0.8444 (m-80) cc_final: 0.8203 (m-80) REVERT: R 284 TYR cc_start: 0.7182 (OUTLIER) cc_final: 0.6880 (p90) REVERT: S 235 TYR cc_start: 0.7271 (OUTLIER) cc_final: 0.6497 (t80) REVERT: C 18 GLN cc_start: 0.7915 (tp40) cc_final: 0.7553 (tp-100) REVERT: C 22 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6843 (mt-10) outliers start: 31 outliers final: 17 residues processed: 189 average time/residue: 0.1023 time to fit residues: 26.1606 Evaluate side-chains 182 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain C residue 37 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 28 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 15 optimal weight: 0.0040 chunk 85 optimal weight: 0.7980 chunk 96 optimal weight: 20.0000 chunk 21 optimal weight: 0.8980 chunk 83 optimal weight: 0.0060 chunk 16 optimal weight: 0.0040 chunk 79 optimal weight: 9.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.3020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN R 189 HIS ** S 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.191204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.126657 restraints weight = 10303.529| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.30 r_work: 0.3251 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8984 Z= 0.106 Angle : 0.597 9.909 12167 Z= 0.303 Chirality : 0.042 0.252 1364 Planarity : 0.004 0.047 1542 Dihedral : 5.042 37.118 1245 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.53 % Allowed : 21.82 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.25), residues: 1114 helix: 1.19 (0.29), residues: 355 sheet: -1.01 (0.30), residues: 276 loop : -1.89 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 134 TYR 0.031 0.001 TYR R 284 PHE 0.016 0.001 PHE R 276 TRP 0.011 0.001 TRP B 339 HIS 0.003 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 8981) covalent geometry : angle 0.59678 (12161) SS BOND : bond 0.00052 ( 3) SS BOND : angle 0.67354 ( 6) hydrogen bonds : bond 0.03079 ( 379) hydrogen bonds : angle 4.41553 ( 1104) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7175 (tt0) REVERT: B 234 PHE cc_start: 0.9206 (OUTLIER) cc_final: 0.8965 (m-80) REVERT: B 264 TYR cc_start: 0.9118 (m-80) cc_final: 0.8677 (m-80) REVERT: B 325 MET cc_start: 0.8272 (tpp) cc_final: 0.8031 (tpp) REVERT: R 194 LEU cc_start: 0.8543 (mm) cc_final: 0.8143 (tp) REVERT: R 227 LYS cc_start: 0.7872 (mmmm) cc_final: 0.7282 (mppt) REVERT: S 235 TYR cc_start: 0.7307 (OUTLIER) cc_final: 0.6670 (t80) REVERT: C 18 GLN cc_start: 0.7956 (tp40) cc_final: 0.7647 (tp-100) outliers start: 33 outliers final: 16 residues processed: 196 average time/residue: 0.0971 time to fit residues: 25.8036 Evaluate side-chains 184 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 99 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 76 optimal weight: 0.0030 chunk 91 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN S 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.189010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.124357 restraints weight = 10327.821| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.55 r_work: 0.3187 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8984 Z= 0.132 Angle : 0.610 9.437 12167 Z= 0.310 Chirality : 0.042 0.267 1364 Planarity : 0.004 0.046 1542 Dihedral : 5.057 35.981 1245 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.74 % Allowed : 21.82 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.25), residues: 1114 helix: 1.37 (0.29), residues: 354 sheet: -1.00 (0.31), residues: 276 loop : -1.83 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 134 TYR 0.033 0.001 TYR R 284 PHE 0.013 0.001 PHE R 276 TRP 0.009 0.001 TRP S 47 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8981) covalent geometry : angle 0.61013 (12161) SS BOND : bond 0.00083 ( 3) SS BOND : angle 0.67612 ( 6) hydrogen bonds : bond 0.03128 ( 379) hydrogen bonds : angle 4.38799 ( 1104) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7137 (tt0) REVERT: A 266 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8585 (tp) REVERT: A 273 LEU cc_start: 0.7527 (tt) cc_final: 0.7125 (tt) REVERT: B 146 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8722 (tp) REVERT: B 234 PHE cc_start: 0.9272 (OUTLIER) cc_final: 0.9005 (m-80) REVERT: B 246 ASP cc_start: 0.8439 (m-30) cc_final: 0.8182 (m-30) REVERT: R 194 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8007 (tp) REVERT: R 219 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7834 (tp40) REVERT: R 227 LYS cc_start: 0.7892 (mmmm) cc_final: 0.7295 (mppt) REVERT: S 180 ARG cc_start: 0.8511 (mtm-85) cc_final: 0.7901 (mtt90) REVERT: S 235 TYR cc_start: 0.7162 (OUTLIER) cc_final: 0.6416 (t80) REVERT: C 18 GLN cc_start: 0.7956 (tp40) cc_final: 0.7603 (tp-100) outliers start: 35 outliers final: 19 residues processed: 200 average time/residue: 0.0973 time to fit residues: 26.4703 Evaluate side-chains 192 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 219 GLN Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 7 optimal weight: 4.9990 chunk 62 optimal weight: 20.0000 chunk 65 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 90 optimal weight: 0.3980 chunk 95 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 237 ASN R 68 ASN S 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.187036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.126463 restraints weight = 10347.001| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.38 r_work: 0.3167 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8984 Z= 0.165 Angle : 0.635 13.473 12167 Z= 0.322 Chirality : 0.043 0.285 1364 Planarity : 0.004 0.047 1542 Dihedral : 5.164 34.588 1245 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.39 % Allowed : 22.14 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.25), residues: 1114 helix: 1.33 (0.29), residues: 355 sheet: -1.00 (0.31), residues: 276 loop : -1.80 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 134 TYR 0.034 0.002 TYR R 284 PHE 0.021 0.001 PHE R 117 TRP 0.009 0.001 TRP S 47 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 8981) covalent geometry : angle 0.63521 (12161) SS BOND : bond 0.00121 ( 3) SS BOND : angle 0.72995 ( 6) hydrogen bonds : bond 0.03225 ( 379) hydrogen bonds : angle 4.41329 ( 1104) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 169 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7229 (tt0) REVERT: A 240 MET cc_start: 0.6472 (tpp) cc_final: 0.6183 (tpp) REVERT: A 266 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8596 (tp) REVERT: B 59 TYR cc_start: 0.8853 (m-80) cc_final: 0.8607 (m-80) REVERT: B 146 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8840 (tp) REVERT: B 155 ASN cc_start: 0.7903 (t0) cc_final: 0.7687 (t0) REVERT: B 229 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8020 (pt) REVERT: B 234 PHE cc_start: 0.9363 (OUTLIER) cc_final: 0.9106 (m-80) REVERT: B 246 ASP cc_start: 0.8643 (m-30) cc_final: 0.8332 (m-30) REVERT: R 194 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8011 (tp) REVERT: R 219 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7930 (tm-30) REVERT: S 235 TYR cc_start: 0.7377 (OUTLIER) cc_final: 0.6528 (t80) REVERT: C 18 GLN cc_start: 0.8024 (tp40) cc_final: 0.7656 (tp-100) outliers start: 41 outliers final: 26 residues processed: 197 average time/residue: 0.0992 time to fit residues: 26.4972 Evaluate side-chains 192 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 219 GLN Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 26 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 39 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 63 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 75 GLN B 237 ASN R 68 ASN S 179 GLN S 183 GLN S 194 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.187952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.122307 restraints weight = 10379.688| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.58 r_work: 0.3179 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8984 Z= 0.145 Angle : 0.633 12.921 12167 Z= 0.318 Chirality : 0.043 0.285 1364 Planarity : 0.004 0.049 1542 Dihedral : 5.110 32.994 1245 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.39 % Allowed : 22.78 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.25), residues: 1114 helix: 1.39 (0.29), residues: 357 sheet: -0.95 (0.31), residues: 274 loop : -1.82 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 134 TYR 0.034 0.001 TYR R 284 PHE 0.016 0.001 PHE R 276 TRP 0.009 0.001 TRP B 211 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 8981) covalent geometry : angle 0.63255 (12161) SS BOND : bond 0.00112 ( 3) SS BOND : angle 0.72603 ( 6) hydrogen bonds : bond 0.03123 ( 379) hydrogen bonds : angle 4.37006 ( 1104) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 165 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7152 (tt0) REVERT: A 266 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8584 (tp) REVERT: A 349 LYS cc_start: 0.7792 (tppt) cc_final: 0.7266 (ttpt) REVERT: B 146 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8745 (tp) REVERT: B 155 ASN cc_start: 0.7893 (t0) cc_final: 0.7680 (t0) REVERT: B 229 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.7963 (pt) REVERT: B 234 PHE cc_start: 0.9278 (OUTLIER) cc_final: 0.9043 (m-80) REVERT: B 246 ASP cc_start: 0.8390 (m-30) cc_final: 0.8112 (m-30) REVERT: R 194 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7951 (tp) REVERT: R 219 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7786 (tm-30) REVERT: R 227 LYS cc_start: 0.8066 (mmmm) cc_final: 0.7401 (mppt) REVERT: S 180 ARG cc_start: 0.8420 (mtm-85) cc_final: 0.7885 (mtt90) REVERT: S 235 TYR cc_start: 0.7075 (OUTLIER) cc_final: 0.6253 (t80) REVERT: C 18 GLN cc_start: 0.7980 (tp40) cc_final: 0.7622 (tp-100) outliers start: 41 outliers final: 26 residues processed: 194 average time/residue: 0.0997 time to fit residues: 25.9790 Evaluate side-chains 195 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 219 GLN Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 194 ASN Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 86 optimal weight: 0.7980 chunk 100 optimal weight: 0.1980 chunk 94 optimal weight: 0.4980 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 22 optimal weight: 0.0470 chunk 89 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 55 optimal weight: 10.0000 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN S 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.188692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.123767 restraints weight = 10313.845| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.71 r_work: 0.3170 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8984 Z= 0.119 Angle : 0.620 12.614 12167 Z= 0.311 Chirality : 0.042 0.293 1364 Planarity : 0.004 0.055 1542 Dihedral : 5.078 31.321 1245 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.96 % Allowed : 22.78 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.25), residues: 1114 helix: 1.43 (0.29), residues: 357 sheet: -0.90 (0.31), residues: 274 loop : -1.80 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 134 TYR 0.034 0.001 TYR R 284 PHE 0.031 0.001 PHE R 180 TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS S 167 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8981) covalent geometry : angle 0.61996 (12161) SS BOND : bond 0.00096 ( 3) SS BOND : angle 0.69222 ( 6) hydrogen bonds : bond 0.03007 ( 379) hydrogen bonds : angle 4.29751 ( 1104) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7158 (tt0) REVERT: A 266 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8558 (tp) REVERT: A 349 LYS cc_start: 0.7785 (tppt) cc_final: 0.7238 (ttpt) REVERT: B 146 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8695 (tp) REVERT: B 246 ASP cc_start: 0.8434 (m-30) cc_final: 0.8138 (m-30) REVERT: R 194 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7924 (tp) REVERT: R 219 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7849 (tm-30) REVERT: R 227 LYS cc_start: 0.8041 (mmmm) cc_final: 0.7379 (mppt) REVERT: S 180 ARG cc_start: 0.8445 (mtm-85) cc_final: 0.7963 (mtt90) REVERT: S 235 TYR cc_start: 0.7016 (OUTLIER) cc_final: 0.6232 (t80) outliers start: 37 outliers final: 26 residues processed: 184 average time/residue: 0.0996 time to fit residues: 24.7059 Evaluate side-chains 193 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 103 MET Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 219 GLN Chi-restraints excluded: chain R residue 269 TYR Chi-restraints excluded: chain R residue 280 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 7 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 56 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 78 optimal weight: 0.0970 chunk 99 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 183 GLN S 194 ASN C 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.185942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.118108 restraints weight = 10318.848| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.82 r_work: 0.3107 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8984 Z= 0.211 Angle : 0.670 12.562 12167 Z= 0.340 Chirality : 0.044 0.288 1364 Planarity : 0.004 0.057 1542 Dihedral : 5.365 34.081 1245 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 4.17 % Allowed : 22.67 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.25), residues: 1114 helix: 1.22 (0.28), residues: 362 sheet: -0.99 (0.31), residues: 274 loop : -1.81 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 134 TYR 0.038 0.002 TYR S 235 PHE 0.028 0.002 PHE R 180 TRP 0.011 0.001 TRP S 47 HIS 0.003 0.001 HIS S 167 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 8981) covalent geometry : angle 0.66954 (12161) SS BOND : bond 0.00163 ( 3) SS BOND : angle 0.85963 ( 6) hydrogen bonds : bond 0.03366 ( 379) hydrogen bonds : angle 4.45407 ( 1104) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 164 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7232 (tt0) REVERT: A 266 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8578 (tp) REVERT: A 349 LYS cc_start: 0.7798 (tppt) cc_final: 0.7257 (ttpt) REVERT: B 204 CYS cc_start: 0.8166 (m) cc_final: 0.7588 (t) REVERT: B 229 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8089 (pt) REVERT: B 246 ASP cc_start: 0.8482 (m-30) cc_final: 0.8219 (m-30) REVERT: R 219 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7938 (tm-30) REVERT: R 227 LYS cc_start: 0.8121 (mmmm) cc_final: 0.7463 (mppt) REVERT: S 18 ARG cc_start: 0.7400 (tpp-160) cc_final: 0.6999 (tpp-160) REVERT: S 235 TYR cc_start: 0.7140 (OUTLIER) cc_final: 0.6401 (t80) REVERT: C 18 GLN cc_start: 0.8031 (tp40) cc_final: 0.7663 (tp-100) outliers start: 39 outliers final: 27 residues processed: 191 average time/residue: 0.1079 time to fit residues: 27.4677 Evaluate side-chains 188 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 103 MET Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 219 GLN Chi-restraints excluded: chain R residue 269 TYR Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 194 ASN Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 105 optimal weight: 0.0370 chunk 66 optimal weight: 0.0470 chunk 83 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 37 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 179 GLN S 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.189740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.125061 restraints weight = 10261.616| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.72 r_work: 0.3194 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8984 Z= 0.114 Angle : 0.625 12.658 12167 Z= 0.315 Chirality : 0.043 0.308 1364 Planarity : 0.004 0.047 1542 Dihedral : 5.168 33.975 1245 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.46 % Allowed : 24.71 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.25), residues: 1114 helix: 1.32 (0.29), residues: 363 sheet: -0.94 (0.31), residues: 274 loop : -1.74 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 134 TYR 0.035 0.001 TYR R 284 PHE 0.024 0.001 PHE R 180 TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 8981) covalent geometry : angle 0.62544 (12161) SS BOND : bond 0.00080 ( 3) SS BOND : angle 0.70465 ( 6) hydrogen bonds : bond 0.02972 ( 379) hydrogen bonds : angle 4.30968 ( 1104) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7199 (tt0) REVERT: A 266 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8531 (tp) REVERT: B 204 CYS cc_start: 0.7720 (m) cc_final: 0.7271 (t) REVERT: B 246 ASP cc_start: 0.8360 (m-30) cc_final: 0.8043 (m-30) REVERT: B 264 TYR cc_start: 0.9131 (m-80) cc_final: 0.8694 (m-80) REVERT: R 194 LEU cc_start: 0.8298 (mm) cc_final: 0.8065 (mt) REVERT: R 219 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7932 (tm-30) REVERT: R 227 LYS cc_start: 0.8063 (mmmm) cc_final: 0.7405 (mppt) REVERT: S 180 ARG cc_start: 0.8479 (mtm-85) cc_final: 0.8267 (mtt90) REVERT: S 235 TYR cc_start: 0.6849 (OUTLIER) cc_final: 0.6043 (t80) REVERT: C 18 GLN cc_start: 0.8149 (tp40) cc_final: 0.7687 (tp-100) REVERT: C 22 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6820 (mt-10) outliers start: 23 outliers final: 18 residues processed: 180 average time/residue: 0.1047 time to fit residues: 25.2673 Evaluate side-chains 182 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 219 GLN Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 194 ASN Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 52 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 33 optimal weight: 0.2980 chunk 82 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN S 179 GLN S 183 GLN S 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.188846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.124006 restraints weight = 10188.609| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.64 r_work: 0.3200 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8984 Z= 0.154 Angle : 0.936 59.196 12167 Z= 0.521 Chirality : 0.043 0.316 1364 Planarity : 0.004 0.046 1542 Dihedral : 5.154 33.972 1245 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.78 % Allowed : 24.49 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.25), residues: 1114 helix: 1.32 (0.29), residues: 363 sheet: -0.94 (0.31), residues: 274 loop : -1.75 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 134 TYR 0.036 0.001 TYR R 284 PHE 0.020 0.001 PHE R 180 TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8981) covalent geometry : angle 0.93613 (12161) SS BOND : bond 0.00084 ( 3) SS BOND : angle 0.69993 ( 6) hydrogen bonds : bond 0.02980 ( 379) hydrogen bonds : angle 4.30207 ( 1104) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2742.93 seconds wall clock time: 47 minutes 34.04 seconds (2854.04 seconds total)