Starting phenix.real_space_refine on Tue Mar 3 21:19:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gut_34279/03_2026/8gut_34279_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gut_34279/03_2026/8gut_34279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gut_34279/03_2026/8gut_34279_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gut_34279/03_2026/8gut_34279_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gut_34279/03_2026/8gut_34279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gut_34279/03_2026/8gut_34279.map" } resolution = 2.98 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= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 66 5.16 5 C 5611 2.51 5 N 1498 2.21 5 O 1624 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 8800 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1725 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2594 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2250 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1760 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "R" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'KO8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.30, per 1000 atoms: 0.26 Number of scatterers: 8800 At special positions: 0 Unit cell: (89.6, 116.48, 131.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 F 1 9.00 O 1624 8.00 N 1498 7.00 C 5611 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 174 " - pdb=" SG CYS R 179 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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: 0.65 Conformation dependent library (CDL) restraints added in 298.8 milliseconds 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 12 sheets defined 39.5% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.708A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.639A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 3.934A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.409A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.635A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 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 'C' and resid 8 through 24 removed outlier: 3.560A pdb=" N VAL C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 3.506A 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 Processing helix chain 'R' and resid 21 through 25 removed outlier: 4.506A pdb=" N ASP R 24 " --> pdb=" O PRO R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 61 removed outlier: 4.353A pdb=" N VAL R 36 " --> pdb=" O GLN R 32 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA R 37 " --> pdb=" O LYS R 33 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL R 38 " --> pdb=" O THR R 34 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR R 41 " --> pdb=" O ALA R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 95 removed outlier: 3.582A pdb=" N LEU R 71 " --> pdb=" O LYS R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.726A pdb=" N LEU R 108 " --> pdb=" O ALA R 104 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS R 109 " --> pdb=" O VAL R 105 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE R 110 " --> pdb=" O PHE R 106 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU R 135 " --> pdb=" O ARG R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 171 Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 187 through 224 Processing helix chain 'R' and resid 238 through 271 removed outlier: 3.705A pdb=" N LEU R 254 " --> pdb=" O VAL R 250 " (cutoff:3.500A) Proline residue: R 260 - end of helix removed outlier: 3.814A pdb=" N ALA R 270 " --> pdb=" O ALA R 266 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 300 removed outlier: 3.684A pdb=" N ASN R 291 " --> pdb=" O LEU R 287 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER R 292 " --> pdb=" O CYS R 288 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET R 293 " --> pdb=" O LEU R 289 " (cutoff:3.500A) Proline residue: R 296 - end of helix Processing helix chain 'R' and resid 303 through 319 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.775A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.552A pdb=" N ASP S 90 " --> pdb=" O ARG S 87 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.863A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.123A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.723A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.736A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.573A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.755A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.751A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.946A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.608A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 129 through 130 Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.765A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 446 hydrogen bonds defined for protein. 1269 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: 1.31 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1408 1.31 - 1.44: 2486 1.44 - 1.56: 4997 1.56 - 1.69: 2 1.69 - 1.82: 95 Bond restraints: 8988 Sorted by residual: bond pdb=" C11 KO8 R 401 " pdb=" N2 KO8 R 401 " ideal model delta sigma weight residual 1.398 1.353 0.045 2.00e-02 2.50e+03 5.02e+00 bond pdb=" CB PRO R 184 " pdb=" CG PRO R 184 " ideal model delta sigma weight residual 1.492 1.594 -0.102 5.00e-02 4.00e+02 4.15e+00 bond pdb=" C5 KO8 R 401 " pdb=" C8 KO8 R 401 " ideal model delta sigma weight residual 1.479 1.518 -0.039 2.00e-02 2.50e+03 3.86e+00 bond pdb=" C11 KO8 R 401 " pdb=" N1 KO8 R 401 " ideal model delta sigma weight residual 1.349 1.384 -0.035 2.00e-02 2.50e+03 3.10e+00 bond pdb=" CB PRO A 282 " pdb=" CG PRO A 282 " ideal model delta sigma weight residual 1.492 1.571 -0.079 5.00e-02 4.00e+02 2.49e+00 ... (remaining 8983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 11957 1.72 - 3.44: 175 3.44 - 5.15: 26 5.15 - 6.87: 13 6.87 - 8.59: 7 Bond angle restraints: 12178 Sorted by residual: angle pdb=" CA PRO R 184 " pdb=" N PRO R 184 " pdb=" CD PRO R 184 " ideal model delta sigma weight residual 112.00 104.55 7.45 1.40e+00 5.10e-01 2.83e+01 angle pdb=" CB LYS C 20 " pdb=" CG LYS C 20 " pdb=" CD LYS C 20 " ideal model delta sigma weight residual 111.30 119.89 -8.59 2.30e+00 1.89e-01 1.40e+01 angle pdb=" CA ARG B 129 " pdb=" CB ARG B 129 " pdb=" CG ARG B 129 " ideal model delta sigma weight residual 114.10 120.70 -6.60 2.00e+00 2.50e-01 1.09e+01 angle pdb=" C ALA B 257 " pdb=" N ASP B 258 " pdb=" CA ASP B 258 " ideal model delta sigma weight residual 122.46 126.47 -4.01 1.41e+00 5.03e-01 8.09e+00 angle pdb=" N PRO R 184 " pdb=" CD PRO R 184 " pdb=" CG PRO R 184 " ideal model delta sigma weight residual 103.20 98.99 4.21 1.50e+00 4.44e-01 7.89e+00 ... (remaining 12173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 4545 17.40 - 34.80: 577 34.80 - 52.20: 173 52.20 - 69.60: 23 69.60 - 87.00: 9 Dihedral angle restraints: 5327 sinusoidal: 2043 harmonic: 3284 Sorted by residual: dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 134.89 -41.89 1 1.00e+01 1.00e-02 2.45e+01 dihedral pdb=" CA ARG B 219 " pdb=" C ARG B 219 " pdb=" N GLN B 220 " pdb=" CA GLN B 220 " ideal model delta harmonic sigma weight residual -180.00 -162.41 -17.59 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ASP A 341 " pdb=" CB ASP A 341 " pdb=" CG ASP A 341 " pdb=" OD1 ASP A 341 " ideal model delta sinusoidal sigma weight residual -30.00 -88.28 58.28 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 5324 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1171 0.054 - 0.108: 182 0.108 - 0.163: 34 0.163 - 0.217: 1 0.217 - 0.271: 1 Chirality restraints: 1389 Sorted by residual: chirality pdb=" C21 KO8 R 401 " pdb=" C22 KO8 R 401 " pdb=" C25 KO8 R 401 " pdb=" N4 KO8 R 401 " both_signs ideal model delta sigma weight residual False -2.38 -2.65 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CB THR R 116 " pdb=" CA THR R 116 " pdb=" OG1 THR R 116 " pdb=" CG2 THR R 116 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.51e-01 chirality pdb=" CA ASP B 258 " pdb=" N ASP B 258 " pdb=" C ASP B 258 " pdb=" CB ASP B 258 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.88e-01 ... (remaining 1386 not shown) Planarity restraints: 1526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE R 183 " 0.077 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO R 184 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO R 184 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO R 184 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 38 " 0.042 5.00e-02 4.00e+02 6.44e-02 6.64e+00 pdb=" N PRO B 39 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS R 67 " -0.029 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO R 68 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO R 68 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO R 68 " -0.025 5.00e-02 4.00e+02 ... (remaining 1523 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 302 2.71 - 3.26: 8733 3.26 - 3.80: 14912 3.80 - 4.35: 18223 4.35 - 4.90: 31250 Nonbonded interactions: 73420 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.161 3.040 nonbonded pdb=" OE2 GLU A 14 " pdb=" OG SER S 52 " model vdw 2.206 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.207 3.040 nonbonded pdb=" O SER R 161 " pdb=" OG SER R 165 " model vdw 2.207 3.040 nonbonded pdb=" OG SER B 147 " pdb=" OG SER B 160 " model vdw 2.228 3.040 ... (remaining 73415 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: 0.780 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.890 Find NCS groups from input model: 0.050 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:9.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 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 0.102 8991 Z= 0.152 Angle : 0.583 8.591 12184 Z= 0.296 Chirality : 0.041 0.271 1389 Planarity : 0.005 0.113 1526 Dihedral : 17.079 86.996 3200 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 31.92 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.35 (0.25), residues: 1117 helix: 1.13 (0.26), residues: 414 sheet: -0.79 (0.31), residues: 275 loop : -1.12 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 13 TYR 0.013 0.001 TYR R 190 PHE 0.012 0.001 PHE A 191 TRP 0.007 0.001 TRP B 211 HIS 0.003 0.001 HIS R 62 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 8988) covalent geometry : angle 0.58335 (12178) SS BOND : bond 0.00306 ( 3) SS BOND : angle 0.53527 ( 6) hydrogen bonds : bond 0.17532 ( 446) hydrogen bonds : angle 7.00436 ( 1269) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: B 22 ARG cc_start: 0.7328 (mtt180) cc_final: 0.7092 (mtt180) REVERT: B 61 MET cc_start: 0.7929 (ptm) cc_final: 0.7717 (tmm) REVERT: B 120 ILE cc_start: 0.8111 (mm) cc_final: 0.7812 (mp) REVERT: B 197 ARG cc_start: 0.7846 (tpt170) cc_final: 0.7500 (mmp-170) REVERT: B 219 ARG cc_start: 0.7800 (mmm-85) cc_final: 0.7454 (ttm110) REVERT: B 270 ILE cc_start: 0.8810 (pt) cc_final: 0.8577 (pp) REVERT: B 275 SER cc_start: 0.8204 (p) cc_final: 0.7849 (p) REVERT: S 57 THR cc_start: 0.8417 (p) cc_final: 0.7940 (t) REVERT: S 159 ASN cc_start: 0.7997 (m-40) cc_final: 0.7586 (m-40) REVERT: S 221 LEU cc_start: 0.8233 (tp) cc_final: 0.7928 (tm) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.5286 time to fit residues: 122.1186 Evaluate side-chains 199 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.0970 chunk 106 optimal weight: 0.0770 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS A 331 ASN B 17 GLN B 75 GLN B 220 GLN B 239 ASN B 340 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.136435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.122832 restraints weight = 13587.060| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.23 r_work: 0.3532 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8991 Z= 0.175 Angle : 0.583 8.718 12184 Z= 0.301 Chirality : 0.042 0.140 1389 Planarity : 0.005 0.057 1526 Dihedral : 4.541 36.578 1241 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 5.29 % Allowed : 29.18 % Favored : 65.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.21 (0.25), residues: 1117 helix: 1.33 (0.25), residues: 403 sheet: -0.71 (0.30), residues: 288 loop : -1.08 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 251 TYR 0.013 0.001 TYR R 190 PHE 0.014 0.001 PHE R 94 TRP 0.019 0.001 TRP B 211 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 8988) covalent geometry : angle 0.58315 (12178) SS BOND : bond 0.00501 ( 3) SS BOND : angle 0.62229 ( 6) hydrogen bonds : bond 0.04329 ( 446) hydrogen bonds : angle 5.14690 ( 1269) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 220 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8432 (m-30) cc_final: 0.8143 (m-30) REVERT: B 67 SER cc_start: 0.8519 (OUTLIER) cc_final: 0.8226 (p) REVERT: B 68 ARG cc_start: 0.8546 (ttt180) cc_final: 0.8322 (ttt180) REVERT: B 158 VAL cc_start: 0.7700 (OUTLIER) cc_final: 0.7378 (t) REVERT: B 197 ARG cc_start: 0.8201 (tpt170) cc_final: 0.7892 (mmp-170) REVERT: B 219 ARG cc_start: 0.8089 (mmm-85) cc_final: 0.7709 (ttm110) REVERT: B 270 ILE cc_start: 0.8799 (pt) cc_final: 0.8597 (pp) REVERT: C 29 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7810 (mtmm) REVERT: C 46 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7642 (mppt) REVERT: R 151 LEU cc_start: 0.8062 (mm) cc_final: 0.7800 (mm) REVERT: S 60 TYR cc_start: 0.8452 (m-80) cc_final: 0.8040 (m-80) REVERT: S 159 ASN cc_start: 0.8016 (m-40) cc_final: 0.7598 (m-40) REVERT: S 200 PHE cc_start: 0.8527 (m-80) cc_final: 0.8313 (m-80) REVERT: S 221 LEU cc_start: 0.8320 (tp) cc_final: 0.7828 (tm) REVERT: S 222 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6893 (pm20) outliers start: 50 outliers final: 22 residues processed: 249 average time/residue: 0.5039 time to fit residues: 133.9826 Evaluate side-chains 231 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 204 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain R residue 279 LYS Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 49 optimal weight: 0.0020 chunk 84 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 106 optimal weight: 0.0470 chunk 75 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 overall best weight: 0.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 75 GLN B 220 GLN B 239 ASN R 95 HIS S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.137640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.124140 restraints weight = 13421.914| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.23 r_work: 0.3549 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8991 Z= 0.125 Angle : 0.548 8.721 12184 Z= 0.279 Chirality : 0.041 0.145 1389 Planarity : 0.004 0.050 1526 Dihedral : 4.349 31.597 1241 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 5.39 % Allowed : 29.18 % Favored : 65.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.07 (0.25), residues: 1117 helix: 1.52 (0.26), residues: 403 sheet: -0.70 (0.30), residues: 289 loop : -1.04 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 49 TYR 0.013 0.001 TYR R 190 PHE 0.012 0.001 PHE R 94 TRP 0.016 0.001 TRP B 211 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8988) covalent geometry : angle 0.54802 (12178) SS BOND : bond 0.00294 ( 3) SS BOND : angle 0.68107 ( 6) hydrogen bonds : bond 0.03715 ( 446) hydrogen bonds : angle 4.77254 ( 1269) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 219 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 197 LYS cc_start: 0.8201 (mtmm) cc_final: 0.7452 (mmpt) REVERT: A 225 VAL cc_start: 0.8745 (t) cc_final: 0.8286 (m) REVERT: A 231 ASP cc_start: 0.8355 (m-30) cc_final: 0.8098 (m-30) REVERT: A 243 MET cc_start: 0.7676 (tpp) cc_final: 0.7420 (tpt) REVERT: A 289 GLU cc_start: 0.7699 (pt0) cc_final: 0.7499 (pp20) REVERT: A 337 ASP cc_start: 0.8103 (m-30) cc_final: 0.7885 (m-30) REVERT: B 14 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7374 (mp) REVERT: B 52 ARG cc_start: 0.7599 (mtm180) cc_final: 0.7264 (ttm110) REVERT: B 120 ILE cc_start: 0.8071 (mm) cc_final: 0.7791 (mp) REVERT: B 158 VAL cc_start: 0.7706 (OUTLIER) cc_final: 0.7488 (t) REVERT: B 197 ARG cc_start: 0.8170 (tpt170) cc_final: 0.7824 (mmp-170) REVERT: B 212 ASP cc_start: 0.7986 (t0) cc_final: 0.7645 (t0) REVERT: B 228 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7437 (p0) REVERT: B 270 ILE cc_start: 0.8782 (pt) cc_final: 0.8580 (pp) REVERT: R 26 MET cc_start: 0.6588 (mmp) cc_final: 0.6384 (mmp) REVERT: R 147 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7063 (tmm-80) REVERT: R 151 LEU cc_start: 0.7877 (mm) cc_final: 0.7398 (mm) REVERT: R 157 MET cc_start: 0.7708 (tmm) cc_final: 0.7493 (tpp) REVERT: R 196 LEU cc_start: 0.8051 (mt) cc_final: 0.7795 (mt) REVERT: S 4 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7960 (mt) REVERT: S 7 SER cc_start: 0.7996 (OUTLIER) cc_final: 0.7753 (p) REVERT: S 60 TYR cc_start: 0.8402 (m-80) cc_final: 0.7987 (m-80) REVERT: S 129 THR cc_start: 0.7809 (t) cc_final: 0.7532 (p) REVERT: S 159 ASN cc_start: 0.7988 (m-40) cc_final: 0.7560 (m-40) REVERT: S 200 PHE cc_start: 0.8544 (m-80) cc_final: 0.8319 (m-80) REVERT: S 204 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7607 (mt) REVERT: S 221 LEU cc_start: 0.8358 (tp) cc_final: 0.8008 (tm) REVERT: S 226 THR cc_start: 0.8539 (m) cc_final: 0.8230 (t) outliers start: 51 outliers final: 22 residues processed: 253 average time/residue: 0.4461 time to fit residues: 121.6162 Evaluate side-chains 233 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 204 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain R residue 147 ARG Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 103 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 110 optimal weight: 0.0870 chunk 17 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 109 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 75 GLN B 220 GLN B 239 ASN R 51 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.137446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.123873 restraints weight = 13595.181| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.26 r_work: 0.3533 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8991 Z= 0.155 Angle : 0.566 8.733 12184 Z= 0.290 Chirality : 0.042 0.144 1389 Planarity : 0.004 0.049 1526 Dihedral : 4.425 35.515 1241 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 6.45 % Allowed : 28.65 % Favored : 64.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.10 (0.25), residues: 1117 helix: 1.56 (0.26), residues: 403 sheet: -0.83 (0.30), residues: 274 loop : -1.02 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 13 TYR 0.012 0.001 TYR S 178 PHE 0.016 0.001 PHE R 94 TRP 0.019 0.001 TRP B 211 HIS 0.004 0.001 HIS R 62 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 8988) covalent geometry : angle 0.56581 (12178) SS BOND : bond 0.00472 ( 3) SS BOND : angle 0.54242 ( 6) hydrogen bonds : bond 0.03679 ( 446) hydrogen bonds : angle 4.67232 ( 1269) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 217 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 49 ILE cc_start: 0.7346 (OUTLIER) cc_final: 0.7088 (tt) REVERT: A 53 MET cc_start: 0.8307 (mtm) cc_final: 0.7934 (mtm) REVERT: A 197 LYS cc_start: 0.8233 (mtmm) cc_final: 0.7487 (mmpt) REVERT: A 231 ASP cc_start: 0.8407 (m-30) cc_final: 0.8144 (m-30) REVERT: A 243 MET cc_start: 0.7685 (tpp) cc_final: 0.7454 (tpt) REVERT: A 337 ASP cc_start: 0.8078 (m-30) cc_final: 0.7764 (m-30) REVERT: B 10 GLU cc_start: 0.6836 (tm-30) cc_final: 0.6634 (tm-30) REVERT: B 14 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7404 (mp) REVERT: B 52 ARG cc_start: 0.7594 (mtm180) cc_final: 0.7229 (ttm110) REVERT: B 67 SER cc_start: 0.8497 (OUTLIER) cc_final: 0.8218 (p) REVERT: B 197 ARG cc_start: 0.8209 (tpt170) cc_final: 0.7850 (mmp-170) REVERT: B 212 ASP cc_start: 0.7965 (t0) cc_final: 0.7577 (t0) REVERT: B 217 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7893 (pmt) REVERT: B 228 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7439 (p0) REVERT: B 234 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.8029 (m-80) REVERT: C 46 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7672 (mppt) REVERT: R 151 LEU cc_start: 0.7885 (mm) cc_final: 0.7583 (mm) REVERT: R 153 THR cc_start: 0.8265 (t) cc_final: 0.8037 (t) REVERT: S 7 SER cc_start: 0.7931 (OUTLIER) cc_final: 0.7702 (p) REVERT: S 60 TYR cc_start: 0.8417 (m-80) cc_final: 0.7983 (m-80) REVERT: S 128 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.6851 (mtm) REVERT: S 129 THR cc_start: 0.7800 (t) cc_final: 0.7500 (p) REVERT: S 159 ASN cc_start: 0.7923 (m-40) cc_final: 0.7499 (m-40) REVERT: S 200 PHE cc_start: 0.8548 (m-80) cc_final: 0.8253 (m-80) REVERT: S 218 MET cc_start: 0.7954 (ptm) cc_final: 0.7649 (ptt) REVERT: S 221 LEU cc_start: 0.8497 (tp) cc_final: 0.7997 (tm) REVERT: S 222 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6899 (pm20) REVERT: S 226 THR cc_start: 0.8535 (m) cc_final: 0.8243 (t) outliers start: 61 outliers final: 31 residues processed: 254 average time/residue: 0.4465 time to fit residues: 121.8890 Evaluate side-chains 254 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 213 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain R residue 33 LYS Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 148 ARG Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 42 optimal weight: 0.2980 chunk 78 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 14 optimal weight: 0.0270 chunk 21 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.137529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.123999 restraints weight = 13577.018| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.26 r_work: 0.3542 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8991 Z= 0.142 Angle : 0.569 10.194 12184 Z= 0.288 Chirality : 0.042 0.256 1389 Planarity : 0.004 0.046 1526 Dihedral : 4.392 32.354 1241 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 6.77 % Allowed : 29.18 % Favored : 64.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.02 (0.25), residues: 1117 helix: 1.68 (0.26), residues: 403 sheet: -0.83 (0.29), residues: 278 loop : -1.01 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 13 TYR 0.011 0.001 TYR R 190 PHE 0.018 0.001 PHE R 94 TRP 0.018 0.001 TRP B 211 HIS 0.004 0.001 HIS R 62 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8988) covalent geometry : angle 0.56909 (12178) SS BOND : bond 0.00450 ( 3) SS BOND : angle 0.55526 ( 6) hydrogen bonds : bond 0.03576 ( 446) hydrogen bonds : angle 4.59981 ( 1269) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 222 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7848 (m-30) cc_final: 0.7361 (m-30) REVERT: A 49 ILE cc_start: 0.7350 (OUTLIER) cc_final: 0.7099 (tt) REVERT: A 53 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7801 (mtm) REVERT: A 225 VAL cc_start: 0.8676 (t) cc_final: 0.8306 (m) REVERT: A 231 ASP cc_start: 0.8390 (m-30) cc_final: 0.8143 (m-30) REVERT: A 243 MET cc_start: 0.7650 (tpp) cc_final: 0.7435 (tpt) REVERT: A 337 ASP cc_start: 0.8091 (m-30) cc_final: 0.7744 (m-30) REVERT: B 14 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7374 (mp) REVERT: B 52 ARG cc_start: 0.7554 (mtm180) cc_final: 0.7161 (ttm110) REVERT: B 67 SER cc_start: 0.8499 (OUTLIER) cc_final: 0.8232 (p) REVERT: B 146 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7824 (mt) REVERT: B 155 ASN cc_start: 0.8293 (t0) cc_final: 0.7916 (t0) REVERT: B 197 ARG cc_start: 0.8201 (tpt170) cc_final: 0.7838 (mmp-170) REVERT: B 212 ASP cc_start: 0.7916 (t0) cc_final: 0.7532 (t0) REVERT: B 217 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7900 (pmt) REVERT: B 228 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7661 (p0) REVERT: B 234 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.8008 (m-80) REVERT: R 151 LEU cc_start: 0.7911 (mm) cc_final: 0.7615 (mm) REVERT: S 7 SER cc_start: 0.7941 (OUTLIER) cc_final: 0.7724 (p) REVERT: S 129 THR cc_start: 0.7819 (t) cc_final: 0.7520 (p) REVERT: S 159 ASN cc_start: 0.7922 (m-40) cc_final: 0.7487 (m-40) REVERT: S 221 LEU cc_start: 0.8345 (tp) cc_final: 0.8048 (tm) REVERT: S 226 THR cc_start: 0.8499 (m) cc_final: 0.8215 (t) outliers start: 64 outliers final: 31 residues processed: 257 average time/residue: 0.4210 time to fit residues: 116.8748 Evaluate side-chains 248 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 208 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain R residue 33 LYS Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 206 ARG Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 88 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 93 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 17 GLN B 220 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 95 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.137232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.123364 restraints weight = 13495.591| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.27 r_work: 0.3534 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8991 Z= 0.156 Angle : 0.588 12.460 12184 Z= 0.296 Chirality : 0.042 0.284 1389 Planarity : 0.004 0.046 1526 Dihedral : 4.391 30.010 1241 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 6.34 % Allowed : 29.70 % Favored : 63.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.08 (0.25), residues: 1117 helix: 1.64 (0.26), residues: 403 sheet: -0.87 (0.29), residues: 279 loop : -1.05 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 27 TYR 0.014 0.001 TYR S 60 PHE 0.024 0.002 PHE R 94 TRP 0.019 0.001 TRP B 211 HIS 0.004 0.001 HIS R 62 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8988) covalent geometry : angle 0.58811 (12178) SS BOND : bond 0.00465 ( 3) SS BOND : angle 0.54420 ( 6) hydrogen bonds : bond 0.03618 ( 446) hydrogen bonds : angle 4.61261 ( 1269) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 221 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7857 (m-30) cc_final: 0.7350 (m-30) REVERT: A 49 ILE cc_start: 0.7338 (OUTLIER) cc_final: 0.7095 (tt) REVERT: A 53 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7993 (mtm) REVERT: A 225 VAL cc_start: 0.8678 (t) cc_final: 0.8299 (m) REVERT: A 231 ASP cc_start: 0.8413 (m-30) cc_final: 0.8177 (m-30) REVERT: A 337 ASP cc_start: 0.8077 (m-30) cc_final: 0.7715 (m-30) REVERT: B 10 GLU cc_start: 0.6850 (tm-30) cc_final: 0.6611 (tm-30) REVERT: B 14 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7440 (mp) REVERT: B 52 ARG cc_start: 0.7583 (mtm180) cc_final: 0.7205 (ttm110) REVERT: B 67 SER cc_start: 0.8513 (OUTLIER) cc_final: 0.8251 (p) REVERT: B 146 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7829 (mt) REVERT: B 161 SER cc_start: 0.7999 (t) cc_final: 0.7506 (p) REVERT: B 197 ARG cc_start: 0.8208 (tpt170) cc_final: 0.7873 (mmp-170) REVERT: B 212 ASP cc_start: 0.7890 (t0) cc_final: 0.7511 (t0) REVERT: B 217 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7894 (pmt) REVERT: B 228 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7656 (p0) REVERT: B 234 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.8007 (m-80) REVERT: C 29 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7810 (mtmm) REVERT: R 151 LEU cc_start: 0.7920 (mm) cc_final: 0.7635 (mm) REVERT: R 153 THR cc_start: 0.8225 (t) cc_final: 0.7845 (p) REVERT: S 7 SER cc_start: 0.7979 (OUTLIER) cc_final: 0.7762 (p) REVERT: S 18 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7010 (mmt180) REVERT: S 60 TYR cc_start: 0.8431 (m-80) cc_final: 0.7915 (m-80) REVERT: S 129 THR cc_start: 0.7841 (t) cc_final: 0.7539 (p) REVERT: S 159 ASN cc_start: 0.7891 (m-40) cc_final: 0.7464 (m-40) REVERT: S 221 LEU cc_start: 0.8347 (tp) cc_final: 0.7927 (tm) REVERT: S 222 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6924 (pm20) REVERT: S 226 THR cc_start: 0.8482 (m) cc_final: 0.8216 (t) outliers start: 60 outliers final: 32 residues processed: 254 average time/residue: 0.4504 time to fit residues: 123.1580 Evaluate side-chains 253 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 209 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain R residue 33 LYS Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 148 ARG Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 76 optimal weight: 0.4980 chunk 84 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 82 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 88 optimal weight: 0.0370 chunk 106 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS B 17 GLN B 220 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.138074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.124223 restraints weight = 13454.964| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.26 r_work: 0.3548 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8991 Z= 0.138 Angle : 0.596 10.835 12184 Z= 0.297 Chirality : 0.042 0.281 1389 Planarity : 0.004 0.046 1526 Dihedral : 4.431 33.807 1241 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 5.92 % Allowed : 31.50 % Favored : 62.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.04 (0.25), residues: 1117 helix: 1.70 (0.26), residues: 403 sheet: -0.77 (0.29), residues: 274 loop : -1.12 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 13 TYR 0.015 0.001 TYR S 101 PHE 0.030 0.002 PHE R 94 TRP 0.018 0.001 TRP B 211 HIS 0.004 0.001 HIS R 62 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8988) covalent geometry : angle 0.59629 (12178) SS BOND : bond 0.00446 ( 3) SS BOND : angle 0.59078 ( 6) hydrogen bonds : bond 0.03518 ( 446) hydrogen bonds : angle 4.56046 ( 1269) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 208 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7838 (m-30) cc_final: 0.7395 (m-30) REVERT: A 49 ILE cc_start: 0.7348 (OUTLIER) cc_final: 0.7122 (tt) REVERT: A 231 ASP cc_start: 0.8360 (m-30) cc_final: 0.8134 (m-30) REVERT: A 337 ASP cc_start: 0.8080 (m-30) cc_final: 0.7785 (m-30) REVERT: B 10 GLU cc_start: 0.6859 (tm-30) cc_final: 0.6606 (tm-30) REVERT: B 14 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7395 (mp) REVERT: B 52 ARG cc_start: 0.7581 (mtm180) cc_final: 0.7201 (ttm110) REVERT: B 67 SER cc_start: 0.8515 (OUTLIER) cc_final: 0.8257 (p) REVERT: B 120 ILE cc_start: 0.8079 (mm) cc_final: 0.7524 (mp) REVERT: B 146 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7783 (mt) REVERT: B 161 SER cc_start: 0.7948 (t) cc_final: 0.7443 (p) REVERT: B 197 ARG cc_start: 0.8215 (tpt170) cc_final: 0.7882 (mmp-170) REVERT: B 212 ASP cc_start: 0.7879 (t0) cc_final: 0.7488 (t0) REVERT: B 217 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7893 (pmt) REVERT: B 234 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.8021 (m-80) REVERT: C 46 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7660 (mppt) REVERT: R 151 LEU cc_start: 0.7927 (mm) cc_final: 0.7630 (mm) REVERT: R 153 THR cc_start: 0.8177 (t) cc_final: 0.7782 (p) REVERT: S 7 SER cc_start: 0.7974 (OUTLIER) cc_final: 0.7759 (p) REVERT: S 18 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7025 (mmt180) REVERT: S 30 SER cc_start: 0.8233 (p) cc_final: 0.7781 (t) REVERT: S 60 TYR cc_start: 0.8411 (m-80) cc_final: 0.7899 (m-80) REVERT: S 72 ARG cc_start: 0.8348 (ptm160) cc_final: 0.8077 (ptm160) REVERT: S 159 ASN cc_start: 0.7847 (m-40) cc_final: 0.7456 (m-40) REVERT: S 221 LEU cc_start: 0.8338 (tp) cc_final: 0.7920 (tm) REVERT: S 222 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6878 (pm20) REVERT: S 226 THR cc_start: 0.8482 (m) cc_final: 0.8246 (t) outliers start: 56 outliers final: 28 residues processed: 243 average time/residue: 0.4703 time to fit residues: 122.8110 Evaluate side-chains 242 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain R residue 26 MET Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 13 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 73 optimal weight: 0.4980 chunk 98 optimal weight: 0.3980 chunk 68 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS B 17 GLN B 220 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.137386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.123780 restraints weight = 13485.730| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.25 r_work: 0.3538 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8991 Z= 0.158 Angle : 0.607 10.236 12184 Z= 0.304 Chirality : 0.043 0.280 1389 Planarity : 0.004 0.046 1526 Dihedral : 4.533 33.619 1241 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 5.81 % Allowed : 31.18 % Favored : 63.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.09 (0.25), residues: 1117 helix: 1.68 (0.26), residues: 404 sheet: -0.82 (0.29), residues: 274 loop : -1.16 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 13 TYR 0.012 0.001 TYR S 178 PHE 0.035 0.002 PHE R 94 TRP 0.019 0.001 TRP B 211 HIS 0.005 0.001 HIS R 62 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 8988) covalent geometry : angle 0.60732 (12178) SS BOND : bond 0.00478 ( 3) SS BOND : angle 0.52776 ( 6) hydrogen bonds : bond 0.03562 ( 446) hydrogen bonds : angle 4.58555 ( 1269) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 213 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7854 (m-30) cc_final: 0.7416 (m-30) REVERT: A 190 THR cc_start: 0.8512 (m) cc_final: 0.8312 (p) REVERT: A 231 ASP cc_start: 0.8408 (m-30) cc_final: 0.8181 (m-30) REVERT: A 309 ASP cc_start: 0.7900 (t0) cc_final: 0.7551 (t0) REVERT: A 337 ASP cc_start: 0.8125 (m-30) cc_final: 0.7813 (m-30) REVERT: B 3 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6704 (tm-30) REVERT: B 10 GLU cc_start: 0.6850 (tm-30) cc_final: 0.6632 (tm-30) REVERT: B 14 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7279 (mp) REVERT: B 52 ARG cc_start: 0.7603 (mtm180) cc_final: 0.7233 (ttm110) REVERT: B 67 SER cc_start: 0.8442 (OUTLIER) cc_final: 0.8175 (p) REVERT: B 133 VAL cc_start: 0.7907 (OUTLIER) cc_final: 0.7706 (t) REVERT: B 146 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7800 (mt) REVERT: B 161 SER cc_start: 0.8014 (t) cc_final: 0.7502 (p) REVERT: B 197 ARG cc_start: 0.8234 (tpt170) cc_final: 0.7893 (mmp-170) REVERT: B 212 ASP cc_start: 0.7905 (t0) cc_final: 0.7507 (t0) REVERT: B 228 ASP cc_start: 0.8202 (p0) cc_final: 0.7822 (p0) REVERT: B 234 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.8080 (m-80) REVERT: C 29 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7808 (mtmm) REVERT: C 46 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7668 (mppt) REVERT: R 151 LEU cc_start: 0.7941 (mm) cc_final: 0.7646 (mm) REVERT: R 153 THR cc_start: 0.8179 (t) cc_final: 0.7779 (p) REVERT: S 7 SER cc_start: 0.7971 (OUTLIER) cc_final: 0.7760 (p) REVERT: S 18 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7043 (mmt180) REVERT: S 30 SER cc_start: 0.8245 (p) cc_final: 0.7853 (t) REVERT: S 60 TYR cc_start: 0.8455 (m-80) cc_final: 0.8026 (m-80) REVERT: S 221 LEU cc_start: 0.8340 (tp) cc_final: 0.7951 (tm) REVERT: S 226 THR cc_start: 0.8473 (m) cc_final: 0.8220 (t) outliers start: 55 outliers final: 30 residues processed: 248 average time/residue: 0.4473 time to fit residues: 119.6655 Evaluate side-chains 248 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 208 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain R residue 73 ILE Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 69 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 77 optimal weight: 0.0980 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 0.1980 chunk 88 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS B 17 GLN B 220 GLN R 95 HIS S 39 GLN S 167 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.137828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.123937 restraints weight = 13332.648| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.26 r_work: 0.3545 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8991 Z= 0.147 Angle : 0.616 10.099 12184 Z= 0.306 Chirality : 0.043 0.256 1389 Planarity : 0.004 0.047 1526 Dihedral : 4.528 32.346 1241 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.97 % Allowed : 32.03 % Favored : 63.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.10 (0.25), residues: 1117 helix: 1.68 (0.26), residues: 404 sheet: -0.85 (0.29), residues: 279 loop : -1.14 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 13 TYR 0.011 0.001 TYR S 178 PHE 0.034 0.002 PHE R 94 TRP 0.019 0.001 TRP B 211 HIS 0.005 0.001 HIS R 62 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8988) covalent geometry : angle 0.61591 (12178) SS BOND : bond 0.00458 ( 3) SS BOND : angle 0.55172 ( 6) hydrogen bonds : bond 0.03534 ( 446) hydrogen bonds : angle 4.55366 ( 1269) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 212 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7851 (m-30) cc_final: 0.7427 (m-30) REVERT: A 53 MET cc_start: 0.7578 (mtm) cc_final: 0.7367 (mtp) REVERT: A 231 ASP cc_start: 0.8401 (m-30) cc_final: 0.8170 (m-30) REVERT: A 309 ASP cc_start: 0.7870 (t0) cc_final: 0.7514 (t0) REVERT: A 337 ASP cc_start: 0.8190 (m-30) cc_final: 0.7872 (m-30) REVERT: B 3 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6694 (tm-30) REVERT: B 10 GLU cc_start: 0.6844 (tm-30) cc_final: 0.6628 (tm-30) REVERT: B 14 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7272 (mp) REVERT: B 52 ARG cc_start: 0.7614 (mtm180) cc_final: 0.7242 (ttm110) REVERT: B 67 SER cc_start: 0.8521 (OUTLIER) cc_final: 0.8262 (p) REVERT: B 133 VAL cc_start: 0.7909 (OUTLIER) cc_final: 0.7699 (t) REVERT: B 146 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7794 (mt) REVERT: B 161 SER cc_start: 0.8019 (t) cc_final: 0.7689 (p) REVERT: B 197 ARG cc_start: 0.8244 (tpt170) cc_final: 0.7906 (mmp-170) REVERT: B 205 ASP cc_start: 0.7627 (p0) cc_final: 0.7363 (p0) REVERT: B 212 ASP cc_start: 0.7903 (t0) cc_final: 0.7523 (t0) REVERT: B 234 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.8068 (m-80) REVERT: C 29 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7799 (mtmm) REVERT: C 46 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7671 (mppt) REVERT: R 151 LEU cc_start: 0.7945 (mm) cc_final: 0.7649 (mm) REVERT: R 153 THR cc_start: 0.8166 (t) cc_final: 0.7766 (p) REVERT: S 7 SER cc_start: 0.7969 (OUTLIER) cc_final: 0.7754 (p) REVERT: S 18 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7066 (mmt180) REVERT: S 30 SER cc_start: 0.8246 (p) cc_final: 0.7849 (t) REVERT: S 60 TYR cc_start: 0.8425 (m-80) cc_final: 0.8013 (m-80) REVERT: S 129 THR cc_start: 0.7796 (t) cc_final: 0.7555 (p) REVERT: S 179 ARG cc_start: 0.6558 (OUTLIER) cc_final: 0.5947 (mtt180) REVERT: S 221 LEU cc_start: 0.8302 (tp) cc_final: 0.7921 (tm) REVERT: S 226 THR cc_start: 0.8477 (m) cc_final: 0.8223 (t) outliers start: 47 outliers final: 29 residues processed: 242 average time/residue: 0.4752 time to fit residues: 123.1554 Evaluate side-chains 241 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 201 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain R residue 73 ILE Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 179 ARG Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 54 optimal weight: 3.9990 chunk 90 optimal weight: 0.0010 chunk 87 optimal weight: 5.9990 chunk 74 optimal weight: 0.0010 chunk 50 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 103 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 0.1980 chunk 82 optimal weight: 0.5980 overall best weight: 0.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 220 GLN B 340 ASN R 98 HIS S 39 GLN S 167 GLN S 182 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.139947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.126151 restraints weight = 13412.632| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.28 r_work: 0.3576 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8991 Z= 0.118 Angle : 0.618 12.615 12184 Z= 0.303 Chirality : 0.042 0.241 1389 Planarity : 0.004 0.046 1526 Dihedral : 4.465 30.196 1241 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.44 % Allowed : 33.40 % Favored : 62.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.03 (0.25), residues: 1117 helix: 1.76 (0.26), residues: 404 sheet: -0.66 (0.29), residues: 276 loop : -1.13 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 13 TYR 0.011 0.001 TYR S 60 PHE 0.026 0.001 PHE R 197 TRP 0.018 0.001 TRP B 211 HIS 0.005 0.001 HIS R 62 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8988) covalent geometry : angle 0.61752 (12178) SS BOND : bond 0.00395 ( 3) SS BOND : angle 0.60091 ( 6) hydrogen bonds : bond 0.03335 ( 446) hydrogen bonds : angle 4.47524 ( 1269) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 208 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7756 (m-30) cc_final: 0.7328 (m-30) REVERT: A 39 LEU cc_start: 0.8325 (mt) cc_final: 0.8102 (mm) REVERT: A 231 ASP cc_start: 0.8351 (m-30) cc_final: 0.8126 (m-30) REVERT: A 309 ASP cc_start: 0.7833 (t0) cc_final: 0.7468 (t0) REVERT: A 337 ASP cc_start: 0.8163 (m-30) cc_final: 0.7873 (m-30) REVERT: B 3 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6672 (tm-30) REVERT: B 14 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7236 (mp) REVERT: B 52 ARG cc_start: 0.7564 (mtm180) cc_final: 0.7208 (ttm110) REVERT: B 100 VAL cc_start: 0.8792 (p) cc_final: 0.8350 (t) REVERT: B 120 ILE cc_start: 0.7997 (mm) cc_final: 0.7463 (mp) REVERT: B 133 VAL cc_start: 0.7887 (OUTLIER) cc_final: 0.7677 (t) REVERT: B 146 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7748 (mt) REVERT: B 161 SER cc_start: 0.7962 (t) cc_final: 0.7443 (p) REVERT: B 197 ARG cc_start: 0.8215 (tpt170) cc_final: 0.7890 (mmp-170) REVERT: B 205 ASP cc_start: 0.7543 (p0) cc_final: 0.7322 (p0) REVERT: B 212 ASP cc_start: 0.7876 (t0) cc_final: 0.7471 (t0) REVERT: B 219 ARG cc_start: 0.8029 (mmm-85) cc_final: 0.7717 (ttm110) REVERT: B 234 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.8029 (m-80) REVERT: C 46 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7660 (mppt) REVERT: R 26 MET cc_start: 0.5266 (mmp) cc_final: 0.4515 (mmp) REVERT: R 151 LEU cc_start: 0.7955 (mm) cc_final: 0.7666 (mm) REVERT: R 153 THR cc_start: 0.8128 (t) cc_final: 0.7726 (p) REVERT: S 7 SER cc_start: 0.7973 (OUTLIER) cc_final: 0.7749 (p) REVERT: S 18 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7046 (mmt180) REVERT: S 30 SER cc_start: 0.8261 (p) cc_final: 0.7802 (t) REVERT: S 72 ARG cc_start: 0.8340 (ptm160) cc_final: 0.8060 (ptm160) REVERT: S 129 THR cc_start: 0.7681 (t) cc_final: 0.7444 (p) REVERT: S 179 ARG cc_start: 0.6283 (OUTLIER) cc_final: 0.5648 (mtt180) REVERT: S 221 LEU cc_start: 0.8231 (tp) cc_final: 0.7931 (tm) outliers start: 42 outliers final: 23 residues processed: 237 average time/residue: 0.4414 time to fit residues: 112.8078 Evaluate side-chains 234 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 202 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 179 ARG Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 63 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 0.0020 chunk 51 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 155 ASN S 39 GLN S 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.138522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.124828 restraints weight = 13347.393| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.26 r_work: 0.3556 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8991 Z= 0.151 Angle : 0.633 12.530 12184 Z= 0.314 Chirality : 0.043 0.311 1389 Planarity : 0.004 0.047 1526 Dihedral : 4.481 31.671 1241 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.59 % Allowed : 34.57 % Favored : 61.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.00 (0.25), residues: 1117 helix: 1.70 (0.26), residues: 404 sheet: -0.62 (0.29), residues: 284 loop : -1.18 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 13 TYR 0.012 0.001 TYR S 178 PHE 0.038 0.002 PHE R 94 TRP 0.019 0.001 TRP B 211 HIS 0.005 0.001 HIS R 62 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 8988) covalent geometry : angle 0.63349 (12178) SS BOND : bond 0.00448 ( 3) SS BOND : angle 0.53393 ( 6) hydrogen bonds : bond 0.03446 ( 446) hydrogen bonds : angle 4.51174 ( 1269) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3386.43 seconds wall clock time: 58 minutes 30.62 seconds (3510.62 seconds total)