Starting phenix.real_space_refine on Sat Dec 28 00:34:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xy7_33513/12_2024/7xy7_33513.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xy7_33513/12_2024/7xy7_33513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xy7_33513/12_2024/7xy7_33513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xy7_33513/12_2024/7xy7_33513.map" model { file = "/net/cci-nas-00/data/ceres_data/7xy7_33513/12_2024/7xy7_33513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xy7_33513/12_2024/7xy7_33513.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 4481 2.51 5 N 1231 2.21 5 O 1288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Residue "R GLU 217": not complete - not flipped Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7047 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1857 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 396 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain: "R" Number of atoms: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2189 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 271} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "R" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'NEC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.71, per 1000 atoms: 0.67 Number of scatterers: 7047 At special positions: 0 Unit cell: (78.72, 101.76, 134.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 1288 8.00 N 1231 7.00 C 4481 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 78 " - pdb=" SG CYS R 171 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 1.0 seconds 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1694 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 9 sheets defined 46.4% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 4.179A pdb=" N ALA A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.958A pdb=" N GLN A 229 " --> pdb=" O LYS A 226 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS A 230 " --> pdb=" O TRP A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 230' Processing helix chain 'A' and resid 249 through 262 removed outlier: 3.582A pdb=" N SER A 258 " --> pdb=" O ASN A 254 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 removed outlier: 3.629A pdb=" N LEU A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 296 through 299 removed outlier: 4.023A pdb=" N ALA A 299 " --> pdb=" O PRO A 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 296 through 299' Processing helix chain 'A' and resid 314 through 335 removed outlier: 3.631A pdb=" N ARG A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 332 " --> pdb=" O PHE A 328 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 374 removed outlier: 3.671A pdb=" N TYR A 374 " --> pdb=" O HIS A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 removed outlier: 3.653A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.716A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 19 removed outlier: 3.713A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.779A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.703A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'R' and resid 6 through 35 removed outlier: 4.140A pdb=" N LEU R 27 " --> pdb=" O ALA R 23 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL R 28 " --> pdb=" O GLY R 24 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS R 29 " --> pdb=" O ASN R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 70 removed outlier: 3.606A pdb=" N TYR R 44 " --> pdb=" O THR R 40 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N PHE R 45 " --> pdb=" O PRO R 41 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU R 46 " --> pdb=" O THR R 42 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ILE R 61 " --> pdb=" O GLY R 57 " (cutoff:3.500A) Proline residue: R 62 - end of helix removed outlier: 4.397A pdb=" N GLY R 70 " --> pdb=" O THR R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 109 removed outlier: 3.584A pdb=" N LEU R 79 " --> pdb=" O PHE R 75 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE R 80 " --> pdb=" O TYR R 76 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU R 81 " --> pdb=" O GLY R 77 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER R 92 " --> pdb=" O LEU R 88 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE R 93 " --> pdb=" O THR R 89 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE R 107 " --> pdb=" O ARG R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 117 removed outlier: 3.561A pdb=" N LEU R 116 " --> pdb=" O ARG R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 138 Processing helix chain 'R' and resid 139 through 143 Processing helix chain 'R' and resid 172 through 177 removed outlier: 3.512A pdb=" N VAL R 177 " --> pdb=" O PHE R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 183 removed outlier: 3.907A pdb=" N MET R 182 " --> pdb=" O PRO R 178 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL R 183 " --> pdb=" O MET R 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 178 through 183' Processing helix chain 'R' and resid 191 through 218 removed outlier: 3.641A pdb=" N PHE R 206 " --> pdb=" O TYR R 202 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU R 218 " --> pdb=" O GLN R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 260 removed outlier: 3.742A pdb=" N HIS R 231 " --> pdb=" O GLN R 227 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET R 238 " --> pdb=" O LYS R 234 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE R 239 " --> pdb=" O SER R 235 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL R 240 " --> pdb=" O LEU R 236 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE R 243 " --> pdb=" O ILE R 239 " (cutoff:3.500A) Proline residue: R 249 - end of helix Processing helix chain 'R' and resid 260 through 266 removed outlier: 4.457A pdb=" N ASN R 266 " --> pdb=" O ALA R 262 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 281 removed outlier: 3.801A pdb=" N ASN R 273 " --> pdb=" O LYS R 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 291 removed outlier: 3.804A pdb=" N VAL R 285 " --> pdb=" O ALA R 281 " (cutoff:3.500A) Proline residue: R 287 - end of helix Processing helix chain 'R' and resid 294 through 308 Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 207 removed outlier: 7.129A pdb=" N ARG A 35 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE A 238 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU A 37 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL A 240 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU A 39 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N ASP A 242 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.800A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.886A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.254A 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: 6.749A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 7.121A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.659A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.441A 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: 6.926A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.124A 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: 3.834A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 72 through 73 removed outlier: 3.527A pdb=" N THR R 73 " --> pdb=" O VAL R 169 " (cutoff:3.500A) 328 hydrogen bonds defined for protein. 960 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: 1.86 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2296 1.34 - 1.46: 1024 1.46 - 1.57: 3805 1.57 - 1.69: 0 1.69 - 1.81: 65 Bond restraints: 7190 Sorted by residual: bond pdb=" C4 NEC R 501 " pdb=" C5 NEC R 501 " ideal model delta sigma weight residual 1.385 1.471 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C5 NEC R 501 " pdb=" C6 NEC R 501 " ideal model delta sigma weight residual 1.407 1.482 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C8 NEC R 501 " pdb=" N7 NEC R 501 " ideal model delta sigma weight residual 1.302 1.357 -0.055 2.00e-02 2.50e+03 7.65e+00 bond pdb=" C3' NEC R 501 " pdb=" O3' NEC R 501 " ideal model delta sigma weight residual 1.393 1.433 -0.040 2.00e-02 2.50e+03 4.03e+00 bond pdb=" C2' NEC R 501 " pdb=" O2' NEC R 501 " ideal model delta sigma weight residual 1.400 1.434 -0.034 2.00e-02 2.50e+03 2.89e+00 ... (remaining 7185 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 9622 1.94 - 3.89: 104 3.89 - 5.83: 20 5.83 - 7.77: 3 7.77 - 9.72: 3 Bond angle restraints: 9752 Sorted by residual: angle pdb=" C2 NEC R 501 " pdb=" N3 NEC R 501 " pdb=" C4 NEC R 501 " ideal model delta sigma weight residual 111.54 120.89 -9.35 3.00e+00 1.11e-01 9.71e+00 angle pdb=" CA LEU B 198 " pdb=" CB LEU B 198 " pdb=" CG LEU B 198 " ideal model delta sigma weight residual 116.30 126.02 -9.72 3.50e+00 8.16e-02 7.70e+00 angle pdb=" C5 NEC R 501 " pdb=" C4 NEC R 501 " pdb=" N3 NEC R 501 " ideal model delta sigma weight residual 126.75 118.68 8.07 3.00e+00 1.11e-01 7.23e+00 angle pdb=" CA GLN B 17 " pdb=" CB GLN B 17 " pdb=" CG GLN B 17 " ideal model delta sigma weight residual 114.10 119.35 -5.25 2.00e+00 2.50e-01 6.89e+00 angle pdb=" CB ARG A 339 " pdb=" CG ARG A 339 " pdb=" CD ARG A 339 " ideal model delta sigma weight residual 111.30 117.23 -5.93 2.30e+00 1.89e-01 6.64e+00 ... (remaining 9747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 4180 35.44 - 70.87: 112 70.87 - 106.31: 4 106.31 - 141.74: 0 141.74 - 177.18: 1 Dihedral angle restraints: 4297 sinusoidal: 1686 harmonic: 2611 Sorted by residual: dihedral pdb=" CB CYS R 78 " pdb=" SG CYS R 78 " pdb=" SG CYS R 171 " pdb=" CB CYS R 171 " ideal model delta sinusoidal sigma weight residual 93.00 162.51 -69.51 1 1.00e+01 1.00e-02 6.24e+01 dihedral pdb=" CB GLU R 217 " pdb=" CG GLU R 217 " pdb=" CD GLU R 217 " pdb=" OE1 GLU R 217 " ideal model delta sinusoidal sigma weight residual 0.00 177.18 -177.18 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CA CYS R 171 " pdb=" C CYS R 171 " pdb=" N LEU R 172 " pdb=" CA LEU R 172 " ideal model delta harmonic sigma weight residual 180.00 161.32 18.68 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 4294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 767 0.037 - 0.074: 260 0.074 - 0.111: 67 0.111 - 0.149: 23 0.149 - 0.186: 1 Chirality restraints: 1118 Sorted by residual: chirality pdb=" C2' NEC R 501 " pdb=" C1' NEC R 501 " pdb=" C3' NEC R 501 " pdb=" O2' NEC R 501 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.62e-01 chirality pdb=" CA PRO R 249 " pdb=" N PRO R 249 " pdb=" C PRO R 249 " pdb=" CB PRO R 249 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ASP B 163 " pdb=" N ASP B 163 " pdb=" C ASP B 163 " pdb=" CB ASP B 163 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 1115 not shown) Planarity restraints: 1239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO R 193 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO R 194 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO R 194 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 194 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 314 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.83e+00 pdb=" N PRO A 315 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 315 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 315 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 118 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.59e+00 pdb=" CG ASP B 118 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASP B 118 " 0.008 2.00e-02 2.50e+03 pdb=" OD2 ASP B 118 " 0.008 2.00e-02 2.50e+03 ... (remaining 1236 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 141 2.69 - 3.24: 6499 3.24 - 3.80: 10479 3.80 - 4.35: 13048 4.35 - 4.90: 22273 Nonbonded interactions: 52440 Sorted by model distance: nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.141 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.258 3.040 nonbonded pdb=" OG1 THR B 173 " pdb=" OE1 GLN B 175 " model vdw 2.259 3.040 nonbonded pdb=" OG SER A 6 " pdb=" OE1 GLU A 8 " model vdw 2.260 3.040 nonbonded pdb=" O ALA A 41 " pdb=" OG SER A 44 " model vdw 2.276 3.040 ... (remaining 52435 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 19.810 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 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 : 0.003 0.086 7190 Z= 0.218 Angle : 0.576 9.715 9752 Z= 0.307 Chirality : 0.042 0.186 1118 Planarity : 0.004 0.041 1239 Dihedral : 15.857 177.175 2600 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.40 % Allowed : 17.72 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.29), residues: 881 helix: 1.98 (0.28), residues: 369 sheet: 0.61 (0.43), residues: 168 loop : -0.72 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.003 0.001 HIS B 54 PHE 0.020 0.001 PHE A 215 TYR 0.008 0.001 TYR R 104 ARG 0.007 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 170 time to evaluate : 0.791 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 171 average time/residue: 0.2838 time to fit residues: 59.7746 Evaluate side-chains 166 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 0.0370 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.0736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7190 Z= 0.220 Angle : 0.508 7.334 9752 Z= 0.275 Chirality : 0.042 0.129 1118 Planarity : 0.004 0.053 1239 Dihedral : 4.307 22.716 1003 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.91 % Allowed : 15.74 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.29), residues: 881 helix: 2.20 (0.27), residues: 381 sheet: 0.65 (0.43), residues: 168 loop : -0.63 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 99 HIS 0.003 0.001 HIS G 44 PHE 0.013 0.001 PHE A 215 TYR 0.008 0.001 TYR A 322 ARG 0.005 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 0.755 Fit side-chains REVERT: B 239 ASN cc_start: 0.7618 (m-40) cc_final: 0.7389 (m-40) REVERT: B 298 ASP cc_start: 0.7368 (t70) cc_final: 0.7066 (t70) REVERT: R 272 MET cc_start: 0.7264 (mmm) cc_final: 0.6989 (tmm) outliers start: 22 outliers final: 15 residues processed: 179 average time/residue: 0.3166 time to fit residues: 68.3225 Evaluate side-chains 188 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 238 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7190 Z= 0.288 Angle : 0.525 8.462 9752 Z= 0.284 Chirality : 0.043 0.127 1118 Planarity : 0.004 0.043 1239 Dihedral : 4.161 18.510 999 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.84 % Allowed : 16.14 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.29), residues: 881 helix: 2.20 (0.27), residues: 381 sheet: 0.73 (0.44), residues: 161 loop : -0.68 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.003 0.001 HIS G 44 PHE 0.017 0.002 PHE B 235 TYR 0.011 0.001 TYR R 10 ARG 0.005 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 0.720 Fit side-chains revert: symmetry clash REVERT: B 114 CYS cc_start: 0.8471 (t) cc_final: 0.8122 (t) REVERT: B 239 ASN cc_start: 0.7606 (m-40) cc_final: 0.7365 (m-40) REVERT: B 283 ARG cc_start: 0.8435 (tpt90) cc_final: 0.8054 (tpt90) REVERT: B 298 ASP cc_start: 0.7436 (t70) cc_final: 0.6989 (t70) outliers start: 29 outliers final: 24 residues processed: 188 average time/residue: 0.2813 time to fit residues: 64.6046 Evaluate side-chains 200 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 238 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 85 optimal weight: 0.2980 chunk 76 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7190 Z= 0.226 Angle : 0.492 8.555 9752 Z= 0.266 Chirality : 0.041 0.128 1118 Planarity : 0.004 0.041 1239 Dihedral : 4.028 18.034 999 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.23 % Allowed : 17.33 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.29), residues: 881 helix: 2.29 (0.27), residues: 381 sheet: 0.76 (0.44), residues: 160 loop : -0.69 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.003 0.001 HIS G 44 PHE 0.013 0.001 PHE B 199 TYR 0.009 0.001 TYR R 10 ARG 0.006 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 178 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: A 330 ARG cc_start: 0.7355 (ttm-80) cc_final: 0.7097 (ttm170) REVERT: B 114 CYS cc_start: 0.8444 (t) cc_final: 0.8064 (t) REVERT: B 239 ASN cc_start: 0.7620 (m-40) cc_final: 0.7356 (m-40) REVERT: B 245 SER cc_start: 0.8436 (p) cc_final: 0.8144 (m) REVERT: B 254 ASP cc_start: 0.7665 (t0) cc_final: 0.7457 (t0) REVERT: B 298 ASP cc_start: 0.7502 (t70) cc_final: 0.6960 (t70) REVERT: R 177 VAL cc_start: 0.7930 (OUTLIER) cc_final: 0.7701 (m) outliers start: 32 outliers final: 24 residues processed: 188 average time/residue: 0.2914 time to fit residues: 67.2175 Evaluate side-chains 203 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 238 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 0.0670 chunk 72 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7190 Z= 0.235 Angle : 0.493 8.563 9752 Z= 0.267 Chirality : 0.042 0.125 1118 Planarity : 0.004 0.041 1239 Dihedral : 3.981 17.008 999 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.84 % Allowed : 17.99 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.29), residues: 881 helix: 2.30 (0.27), residues: 381 sheet: 0.80 (0.44), residues: 155 loop : -0.73 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.003 0.001 HIS G 44 PHE 0.016 0.002 PHE A 215 TYR 0.009 0.001 TYR R 10 ARG 0.005 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: A 330 ARG cc_start: 0.7373 (ttm-80) cc_final: 0.7094 (ttm170) REVERT: B 114 CYS cc_start: 0.8453 (t) cc_final: 0.8081 (t) REVERT: B 239 ASN cc_start: 0.7591 (m-40) cc_final: 0.7377 (m-40) REVERT: B 245 SER cc_start: 0.8402 (p) cc_final: 0.8123 (m) REVERT: B 298 ASP cc_start: 0.7403 (t70) cc_final: 0.6887 (t70) REVERT: R 177 VAL cc_start: 0.7918 (OUTLIER) cc_final: 0.7710 (m) REVERT: R 224 THR cc_start: 0.6812 (t) cc_final: 0.6277 (p) REVERT: R 227 GLN cc_start: 0.7282 (mt0) cc_final: 0.7062 (mt0) outliers start: 29 outliers final: 25 residues processed: 190 average time/residue: 0.2770 time to fit residues: 64.3310 Evaluate side-chains 201 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 238 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 0.0870 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7190 Z= 0.236 Angle : 0.501 8.566 9752 Z= 0.267 Chirality : 0.042 0.124 1118 Planarity : 0.004 0.040 1239 Dihedral : 3.953 16.078 999 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.10 % Allowed : 18.39 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.29), residues: 881 helix: 2.33 (0.27), residues: 381 sheet: 0.81 (0.44), residues: 155 loop : -0.70 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.004 0.001 HIS A 340 PHE 0.015 0.002 PHE A 215 TYR 0.009 0.001 TYR A 322 ARG 0.005 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7837 (ttp-170) cc_final: 0.7378 (ttp-170) REVERT: A 372 ARG cc_start: 0.7844 (ttp80) cc_final: 0.7593 (ttp80) REVERT: B 245 SER cc_start: 0.8446 (p) cc_final: 0.8130 (m) REVERT: B 298 ASP cc_start: 0.7545 (t70) cc_final: 0.6935 (t70) REVERT: R 177 VAL cc_start: 0.7931 (OUTLIER) cc_final: 0.7717 (m) outliers start: 31 outliers final: 25 residues processed: 183 average time/residue: 0.2671 time to fit residues: 60.4226 Evaluate side-chains 201 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 238 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7190 Z= 0.338 Angle : 0.557 9.146 9752 Z= 0.298 Chirality : 0.044 0.134 1118 Planarity : 0.004 0.041 1239 Dihedral : 4.215 16.005 999 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.10 % Allowed : 18.52 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.29), residues: 881 helix: 2.12 (0.27), residues: 380 sheet: 0.80 (0.44), residues: 153 loop : -0.69 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 339 HIS 0.004 0.001 HIS G 44 PHE 0.019 0.002 PHE B 235 TYR 0.012 0.001 TYR R 10 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7860 (ttp-170) cc_final: 0.7425 (ttp-170) REVERT: A 319 ARG cc_start: 0.7905 (ttp80) cc_final: 0.7292 (ttm-80) REVERT: A 330 ARG cc_start: 0.7406 (ttm-80) cc_final: 0.7148 (ttm170) REVERT: B 49 ARG cc_start: 0.8018 (mtt-85) cc_final: 0.7703 (mtt180) REVERT: B 245 SER cc_start: 0.8448 (p) cc_final: 0.8180 (m) REVERT: B 298 ASP cc_start: 0.7598 (t70) cc_final: 0.6978 (t70) REVERT: R 177 VAL cc_start: 0.7996 (OUTLIER) cc_final: 0.7778 (m) REVERT: R 227 GLN cc_start: 0.7344 (mt0) cc_final: 0.7105 (mp10) outliers start: 31 outliers final: 27 residues processed: 188 average time/residue: 0.2956 time to fit residues: 67.6976 Evaluate side-chains 203 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 238 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 41 optimal weight: 0.2980 chunk 7 optimal weight: 0.2980 chunk 66 optimal weight: 0.0010 chunk 77 optimal weight: 0.0980 chunk 81 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 overall best weight: 0.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7190 Z= 0.147 Angle : 0.479 8.775 9752 Z= 0.254 Chirality : 0.041 0.132 1118 Planarity : 0.003 0.038 1239 Dihedral : 3.775 14.745 999 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.04 % Allowed : 20.11 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.29), residues: 881 helix: 2.37 (0.28), residues: 382 sheet: 0.93 (0.44), residues: 152 loop : -0.62 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 99 HIS 0.003 0.000 HIS A 340 PHE 0.018 0.001 PHE A 215 TYR 0.007 0.001 TYR A 322 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7800 (ttp-170) cc_final: 0.7301 (ttp-170) REVERT: A 330 ARG cc_start: 0.7355 (ttm-80) cc_final: 0.7127 (ttm170) REVERT: B 86 THR cc_start: 0.8331 (p) cc_final: 0.8121 (p) REVERT: B 114 CYS cc_start: 0.8423 (t) cc_final: 0.8040 (t) REVERT: B 245 SER cc_start: 0.8330 (p) cc_final: 0.8054 (m) REVERT: B 298 ASP cc_start: 0.7482 (t70) cc_final: 0.6800 (t70) REVERT: R 177 VAL cc_start: 0.7833 (OUTLIER) cc_final: 0.7623 (m) outliers start: 23 outliers final: 18 residues processed: 176 average time/residue: 0.2474 time to fit residues: 54.9658 Evaluate side-chains 181 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 238 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 74 optimal weight: 0.0060 chunk 78 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7190 Z= 0.218 Angle : 0.504 7.056 9752 Z= 0.271 Chirality : 0.042 0.136 1118 Planarity : 0.003 0.040 1239 Dihedral : 3.808 14.460 999 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.31 % Allowed : 20.37 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.29), residues: 881 helix: 2.31 (0.27), residues: 382 sheet: 0.93 (0.44), residues: 152 loop : -0.58 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.003 0.001 HIS A 340 PHE 0.016 0.001 PHE A 215 TYR 0.008 0.001 TYR A 322 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7824 (ttp-170) cc_final: 0.7337 (ttp-170) REVERT: A 330 ARG cc_start: 0.7386 (ttm-80) cc_final: 0.7155 (ttm170) REVERT: B 245 SER cc_start: 0.8383 (p) cc_final: 0.8097 (m) REVERT: B 298 ASP cc_start: 0.7568 (t70) cc_final: 0.7273 (t70) REVERT: R 177 VAL cc_start: 0.7925 (OUTLIER) cc_final: 0.7723 (m) outliers start: 25 outliers final: 21 residues processed: 180 average time/residue: 0.2943 time to fit residues: 65.0042 Evaluate side-chains 192 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 182 MET Chi-restraints excluded: chain R residue 238 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 7 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 74 optimal weight: 0.0670 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7190 Z= 0.188 Angle : 0.493 6.881 9752 Z= 0.265 Chirality : 0.041 0.135 1118 Planarity : 0.003 0.039 1239 Dihedral : 3.744 14.502 999 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.04 % Allowed : 20.50 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.29), residues: 881 helix: 2.32 (0.27), residues: 382 sheet: 0.85 (0.43), residues: 157 loop : -0.60 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 99 HIS 0.006 0.001 HIS A 213 PHE 0.018 0.001 PHE A 215 TYR 0.008 0.001 TYR A 322 ARG 0.002 0.000 ARG B 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7812 (ttp-170) cc_final: 0.7326 (ttp-170) REVERT: A 330 ARG cc_start: 0.7380 (ttm-80) cc_final: 0.7157 (ttm170) REVERT: B 114 CYS cc_start: 0.8414 (t) cc_final: 0.8076 (t) REVERT: B 245 SER cc_start: 0.8363 (p) cc_final: 0.8072 (m) REVERT: B 298 ASP cc_start: 0.7587 (t70) cc_final: 0.7280 (t70) outliers start: 23 outliers final: 22 residues processed: 170 average time/residue: 0.2669 time to fit residues: 56.6364 Evaluate side-chains 183 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 182 MET Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 238 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.131186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.111963 restraints weight = 10407.278| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.43 r_work: 0.3301 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7190 Z= 0.238 Angle : 0.515 6.912 9752 Z= 0.278 Chirality : 0.042 0.131 1118 Planarity : 0.003 0.040 1239 Dihedral : 3.856 14.651 999 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.04 % Allowed : 20.63 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.29), residues: 881 helix: 2.26 (0.27), residues: 382 sheet: 0.80 (0.43), residues: 158 loop : -0.61 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.006 0.001 HIS A 213 PHE 0.019 0.002 PHE A 215 TYR 0.009 0.001 TYR R 10 ARG 0.004 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2044.42 seconds wall clock time: 38 minutes 28.48 seconds (2308.48 seconds total)