Starting phenix.real_space_refine on Thu Feb 13 09:52:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j20_35940/02_2025/8j20_35940.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j20_35940/02_2025/8j20_35940.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j20_35940/02_2025/8j20_35940.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j20_35940/02_2025/8j20_35940.map" model { file = "/net/cci-nas-00/data/ceres_data/8j20_35940/02_2025/8j20_35940.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j20_35940/02_2025/8j20_35940.cif" } resolution = 3.2 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= 0.020 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 58 5.16 5 Cl 2 4.86 5 C 5634 2.51 5 N 1497 2.21 5 O 1641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8832 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2610 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "B" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1775 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Chain: "C" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1791 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 2 Chain: "D" Number of atoms: 2188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2188 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 13, 'TRANS': 260} Chain breaks: 1 Chain: "E" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 433 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'9T4': 1, 'LEA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.17, per 1000 atoms: 0.59 Number of scatterers: 8832 At special positions: 0 Unit cell: (111.28, 110.24, 122.72, 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) Cl 2 17.00 S 58 16.00 O 1641 8.00 N 1497 7.00 C 5634 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 197 " - pdb=" SG CYS B 267 " distance=2.04 Simple disulfide: pdb=" SG CYS D 88 " - pdb=" SG CYS D 169 " 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: 2.38 Conformation dependent library (CDL) restraints added in 1.1 seconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2092 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 13 sheets defined 37.6% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 15 through 36 removed outlier: 3.595A pdb=" N CYS A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 46 removed outlier: 3.504A pdb=" N ILE A 44 " --> pdb=" O THR A 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 94 removed outlier: 3.936A pdb=" N GLY B 94 " --> pdb=" O SER B 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 91 through 94' Processing helix chain 'B' and resid 100 through 103 removed outlier: 3.551A pdb=" N LYS B 103 " --> pdb=" O ASP B 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 100 through 103' Processing helix chain 'B' and resid 125 through 129 removed outlier: 4.015A pdb=" N THR B 129 " --> pdb=" O SER B 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 6 removed outlier: 3.766A pdb=" N SER C 6 " --> pdb=" O CYS C 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3 through 6' Processing helix chain 'C' and resid 7 through 32 removed outlier: 3.661A pdb=" N ALA C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 54 Processing helix chain 'C' and resid 207 through 212 removed outlier: 4.372A pdb=" N TRP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 255 removed outlier: 3.728A pdb=" N LYS C 248 " --> pdb=" O HIS C 244 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 249 " --> pdb=" O GLU C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.596A pdb=" N GLU C 275 " --> pdb=" O LYS C 271 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER C 281 " --> pdb=" O LYS C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 310 removed outlier: 4.029A pdb=" N ALA C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 351 Processing helix chain 'D' and resid 14 through 46 removed outlier: 3.707A pdb=" N VAL D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) Proline residue: D 30 - end of helix removed outlier: 3.958A pdb=" N VAL D 37 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE D 38 " --> pdb=" O LEU D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 73 removed outlier: 3.623A pdb=" N ASP D 61 " --> pdb=" O LEU D 57 " (cutoff:3.500A) Proline residue: D 69 - end of helix Processing helix chain 'D' and resid 87 through 119 removed outlier: 3.522A pdb=" N TYR D 100 " --> pdb=" O PHE D 96 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR D 102 " --> pdb=" O THR D 98 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALA D 103 " --> pdb=" O ILE D 99 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU D 104 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL D 117 " --> pdb=" O ARG D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 128 through 155 removed outlier: 3.736A pdb=" N VAL D 150 " --> pdb=" O HIS D 146 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE D 153 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU D 154 " --> pdb=" O VAL D 150 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE D 155 " --> pdb=" O TYR D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 211 Proline residue: D 183 - end of helix removed outlier: 3.880A pdb=" N VAL D 195 " --> pdb=" O VAL D 191 " (cutoff:3.500A) Proline residue: D 196 - end of helix Processing helix chain 'D' and resid 216 through 252 removed outlier: 4.438A pdb=" N ARG D 220 " --> pdb=" O SER D 216 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU D 226 " --> pdb=" O ARG D 222 " (cutoff:3.500A) Proline residue: D 240 - end of helix removed outlier: 3.766A pdb=" N TYR D 249 " --> pdb=" O HIS D 245 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE D 250 " --> pdb=" O VAL D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 280 removed outlier: 4.044A pdb=" N VAL D 261 " --> pdb=" O TRP D 257 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) Proline residue: D 273 - end of helix removed outlier: 3.584A pdb=" N PHE D 278 " --> pdb=" O LEU D 274 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER D 280 " --> pdb=" O TYR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 291 removed outlier: 3.826A pdb=" N GLU D 289 " --> pdb=" O ALA D 285 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU D 291 " --> pdb=" O PHE D 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 24 removed outlier: 3.654A pdb=" N GLN E 11 " --> pdb=" O ALA E 7 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN E 24 " --> pdb=" O LYS E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 84 removed outlier: 6.064A pdb=" N LEU A 90 " --> pdb=" O ALA A 103 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA A 103 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE A 92 " --> pdb=" O VAL A 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 122 through 126 removed outlier: 6.407A pdb=" N CYS A 132 " --> pdb=" O GLU A 149 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU A 149 " --> pdb=" O CYS A 132 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE A 134 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG A 145 " --> pdb=" O ASN A 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 167 through 171 removed outlier: 3.524A pdb=" N THR A 189 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASP A 181 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N GLN A 187 " --> pdb=" O ASP A 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.651A pdb=" N PHE A 210 " --> pdb=" O TRP A 222 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN A 231 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP A 223 " --> pdb=" O CYS A 229 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N CYS A 229 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 240 through 243 removed outlier: 3.739A pdb=" N SER A 256 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N THR A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N CYS A 261 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N THR A 274 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU A 263 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN A 270 " --> pdb=" O ASP A 265 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 284 through 289 removed outlier: 4.665A pdb=" N VAL A 287 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU A 297 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N PHE A 289 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU A 295 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N CYS A 305 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL A 318 " --> pdb=" O CYS A 305 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A 307 " --> pdb=" O ALA A 316 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 42 through 45 removed outlier: 3.587A pdb=" N THR B 116 " --> pdb=" O ASP B 111 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 48 through 50 removed outlier: 6.151A pdb=" N GLY B 48 " --> pdb=" O THR B 156 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N MET B 72 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR B 88 " --> pdb=" O MET B 72 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP B 74 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 48 through 50 removed outlier: 6.151A pdb=" N GLY B 48 " --> pdb=" O THR B 156 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE B 148 " --> pdb=" O ARG B 136 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 178 through 179 Processing sheet with id=AB3, first strand: chain 'B' and resid 184 through 185 removed outlier: 3.541A pdb=" N GLY B 263 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU B 212 " --> pdb=" O TYR B 228 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TYR B 228 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP B 214 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 196 through 200 removed outlier: 6.490A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU C 39 " --> pdb=" O CYS C 224 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ALA C 226 " --> pdb=" O LEU C 39 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1143 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: 2.64 Time building geometry restraints manager: 2.71 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: 1425 1.31 - 1.44: 2509 1.44 - 1.56: 5002 1.56 - 1.69: 2 1.69 - 1.82: 84 Bond restraints: 9022 Sorted by residual: bond pdb=" C13 9T4 D 401 " pdb=" C16 9T4 D 401 " ideal model delta sigma weight residual 1.342 1.523 -0.181 2.00e-02 2.50e+03 8.20e+01 bond pdb=" C09 9T4 D 401 " pdb=" C10 9T4 D 401 " ideal model delta sigma weight residual 1.359 1.523 -0.164 2.00e-02 2.50e+03 6.70e+01 bond pdb=" C27 9T4 D 401 " pdb=" C28 9T4 D 401 " ideal model delta sigma weight residual 1.384 1.529 -0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" C26 9T4 D 401 " pdb=" C28 9T4 D 401 " ideal model delta sigma weight residual 1.386 1.529 -0.143 2.00e-02 2.50e+03 5.13e+01 bond pdb=" C24 9T4 D 401 " pdb=" C27 9T4 D 401 " ideal model delta sigma weight residual 1.385 1.528 -0.143 2.00e-02 2.50e+03 5.08e+01 ... (remaining 9017 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.99: 12180 3.99 - 7.99: 37 7.99 - 11.98: 3 11.98 - 15.98: 3 15.98 - 19.97: 3 Bond angle restraints: 12226 Sorted by residual: angle pdb=" C TYR B 273 " pdb=" N PRO B 274 " pdb=" CA PRO B 274 " ideal model delta sigma weight residual 119.84 132.52 -12.68 1.25e+00 6.40e-01 1.03e+02 angle pdb=" N TYR B 273 " pdb=" CA TYR B 273 " pdb=" C TYR B 273 " ideal model delta sigma weight residual 109.81 129.78 -19.97 2.21e+00 2.05e-01 8.17e+01 angle pdb=" C PRO B 274 " pdb=" CA PRO B 274 " pdb=" CB PRO B 274 " ideal model delta sigma weight residual 111.56 124.57 -13.01 1.65e+00 3.67e-01 6.22e+01 angle pdb=" C GLU B 272 " pdb=" N TYR B 273 " pdb=" CA TYR B 273 " ideal model delta sigma weight residual 121.80 135.07 -13.27 2.44e+00 1.68e-01 2.96e+01 angle pdb=" CA PRO B 274 " pdb=" N PRO B 274 " pdb=" CD PRO B 274 " ideal model delta sigma weight residual 112.00 104.86 7.14 1.40e+00 5.10e-01 2.60e+01 ... (remaining 12221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.59: 4776 23.59 - 47.18: 502 47.18 - 70.77: 65 70.77 - 94.37: 9 94.37 - 117.96: 1 Dihedral angle restraints: 5353 sinusoidal: 2103 harmonic: 3250 Sorted by residual: dihedral pdb=" CA TYR B 273 " pdb=" C TYR B 273 " pdb=" N PRO B 274 " pdb=" CA PRO B 274 " ideal model delta harmonic sigma weight residual 180.00 62.04 117.96 0 5.00e+00 4.00e-02 5.57e+02 dihedral pdb=" C TYR B 273 " pdb=" N TYR B 273 " pdb=" CA TYR B 273 " pdb=" CB TYR B 273 " ideal model delta harmonic sigma weight residual -122.60 -150.58 27.98 0 2.50e+00 1.60e-01 1.25e+02 dihedral pdb=" N TYR B 273 " pdb=" C TYR B 273 " pdb=" CA TYR B 273 " pdb=" CB TYR B 273 " ideal model delta harmonic sigma weight residual 122.80 150.30 -27.50 0 2.50e+00 1.60e-01 1.21e+02 ... (remaining 5350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.257: 1380 0.257 - 0.514: 0 0.514 - 0.771: 1 0.771 - 1.028: 0 1.028 - 1.286: 1 Chirality restraints: 1382 Sorted by residual: chirality pdb=" CA TYR B 273 " pdb=" N TYR B 273 " pdb=" C TYR B 273 " pdb=" CB TYR B 273 " both_signs ideal model delta sigma weight residual False 2.51 1.22 1.29 2.00e-01 2.50e+01 4.13e+01 chirality pdb=" CA PRO B 274 " pdb=" N PRO B 274 " pdb=" C PRO B 274 " pdb=" CB PRO B 274 " both_signs ideal model delta sigma weight residual False 2.72 2.07 0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" C08 9T4 D 401 " pdb=" C09 9T4 D 401 " pdb=" C13 9T4 D 401 " pdb=" C17 9T4 D 401 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 1379 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 273 " -0.066 5.00e-02 4.00e+02 9.65e-02 1.49e+01 pdb=" N PRO B 274 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO B 274 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 274 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 272 " 0.058 5.00e-02 4.00e+02 8.75e-02 1.23e+01 pdb=" N PRO D 273 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO D 273 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 273 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 239 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO D 240 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 240 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 240 " -0.026 5.00e-02 4.00e+02 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 675 2.74 - 3.28: 8615 3.28 - 3.82: 14912 3.82 - 4.36: 17012 4.36 - 4.90: 29893 Nonbonded interactions: 71107 Sorted by model distance: nonbonded pdb=" OH TYR B 211 " pdb=" OG SER C 6 " model vdw 2.197 3.040 nonbonded pdb=" OG SER A 342 " pdb=" OD1 ASP A 344 " model vdw 2.206 3.040 nonbonded pdb=" OG SER A 172 " pdb=" OD1 ASP A 174 " model vdw 2.236 3.040 nonbonded pdb=" O SER A 78 " pdb=" OG SER A 78 " model vdw 2.265 3.040 nonbonded pdb=" O LEU D 197 " pdb=" OG SER D 201 " model vdw 2.269 3.040 ... (remaining 71102 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=0.01 max=1.00 mean=0.99 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: 1.120 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.020 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 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 : 0.006 0.181 9022 Z= 0.403 Angle : 0.709 19.972 12226 Z= 0.355 Chirality : 0.057 1.286 1382 Planarity : 0.005 0.097 1544 Dihedral : 17.895 117.958 3252 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.43 % Favored : 95.03 % Rotamer: Outliers : 0.62 % Allowed : 35.69 % Favored : 63.68 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.26), residues: 1107 helix: 1.66 (0.28), residues: 355 sheet: 0.71 (0.33), residues: 243 loop : -1.45 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 15 HIS 0.006 0.001 HIS B 205 PHE 0.017 0.001 PHE A 210 TYR 0.011 0.001 TYR D 202 ARG 0.007 0.000 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 197 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 86 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7726 (mm110) REVERT: A 163 LEU cc_start: 0.7931 (mm) cc_final: 0.7715 (mt) outliers start: 6 outliers final: 3 residues processed: 199 average time/residue: 0.2564 time to fit residues: 66.5219 Evaluate side-chains 195 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 192 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 220 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.0020 chunk 84 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN B 180 GLN B 217 GLN C 195 HIS C 241 ASN D 284 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.157760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.136734 restraints weight = 13009.409| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.28 r_work: 0.3556 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 9022 Z= 0.260 Angle : 0.674 13.397 12226 Z= 0.341 Chirality : 0.046 0.359 1382 Planarity : 0.005 0.062 1544 Dihedral : 6.074 58.363 1268 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.24 % Favored : 94.31 % Rotamer: Outliers : 5.20 % Allowed : 29.76 % Favored : 65.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.26), residues: 1107 helix: 1.37 (0.27), residues: 381 sheet: 0.65 (0.34), residues: 243 loop : -1.52 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 85 HIS 0.006 0.001 HIS A 102 PHE 0.023 0.002 PHE D 95 TYR 0.015 0.002 TYR B 88 ARG 0.006 0.001 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 230 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: A 38 ASP cc_start: 0.6832 (OUTLIER) cc_final: 0.6621 (p0) REVERT: A 61 THR cc_start: 0.5501 (OUTLIER) cc_final: 0.4874 (m) REVERT: A 72 MET cc_start: 0.7063 (mmt) cc_final: 0.6733 (mmt) REVERT: A 140 ARG cc_start: 0.7634 (mtp85) cc_final: 0.7299 (mmp80) REVERT: A 269 ASP cc_start: 0.7812 (t0) cc_final: 0.7533 (t0) REVERT: A 297 LEU cc_start: 0.8278 (mp) cc_final: 0.8074 (mp) REVERT: A 326 VAL cc_start: 0.8047 (t) cc_final: 0.7700 (p) REVERT: B 177 VAL cc_start: 0.8105 (m) cc_final: 0.7891 (p) REVERT: B 179 THR cc_start: 0.8297 (p) cc_final: 0.8064 (t) REVERT: B 237 VAL cc_start: 0.8071 (t) cc_final: 0.7841 (p) REVERT: B 268 MET cc_start: 0.8257 (ttm) cc_final: 0.7923 (ttm) REVERT: C 14 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7397 (mt-10) REVERT: C 200 ASP cc_start: 0.8030 (t0) cc_final: 0.7757 (t0) REVERT: C 283 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7887 (mp) REVERT: C 306 GLN cc_start: 0.6342 (mm110) cc_final: 0.6038 (mm110) REVERT: C 316 THR cc_start: 0.7499 (p) cc_final: 0.7206 (t) REVERT: D 29 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7308 (mt) REVERT: D 56 ASN cc_start: 0.7353 (m-40) cc_final: 0.7093 (m-40) outliers start: 50 outliers final: 25 residues processed: 255 average time/residue: 0.2327 time to fit residues: 79.5350 Evaluate side-chains 241 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 290 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 chunk 88 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3901 r_free = 0.3901 target = 0.151728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.130465 restraints weight = 13064.868| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.21 r_work: 0.3485 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9022 Z= 0.276 Angle : 0.655 13.729 12226 Z= 0.330 Chirality : 0.046 0.280 1382 Planarity : 0.005 0.056 1544 Dihedral : 5.927 53.153 1264 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.15 % Favored : 94.40 % Rotamer: Outliers : 5.52 % Allowed : 29.97 % Favored : 64.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.25), residues: 1107 helix: 1.14 (0.27), residues: 391 sheet: 0.23 (0.33), residues: 257 loop : -1.52 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 180 HIS 0.004 0.001 HIS A 102 PHE 0.018 0.002 PHE A 210 TYR 0.016 0.002 TYR B 141 ARG 0.016 0.001 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 215 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6910 (p0) REVERT: A 112 MET cc_start: 0.7969 (ptp) cc_final: 0.7582 (ptp) REVERT: A 135 TYR cc_start: 0.8975 (m-80) cc_final: 0.8524 (m-80) REVERT: A 269 ASP cc_start: 0.7752 (t0) cc_final: 0.7427 (t0) REVERT: B 177 VAL cc_start: 0.8213 (m) cc_final: 0.7976 (p) REVERT: B 179 THR cc_start: 0.8257 (p) cc_final: 0.8031 (t) REVERT: B 237 VAL cc_start: 0.8053 (t) cc_final: 0.7843 (p) REVERT: B 268 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7978 (ttp) REVERT: C 17 LYS cc_start: 0.8351 (mttm) cc_final: 0.8095 (mmtm) REVERT: C 197 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7750 (mttm) REVERT: C 200 ASP cc_start: 0.8110 (t0) cc_final: 0.7761 (t0) REVERT: C 245 GLU cc_start: 0.7302 (tm-30) cc_final: 0.7028 (tm-30) REVERT: C 306 GLN cc_start: 0.6355 (mm110) cc_final: 0.5955 (mm110) REVERT: C 316 THR cc_start: 0.7548 (p) cc_final: 0.7261 (t) REVERT: D 29 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7109 (mt) REVERT: D 52 VAL cc_start: 0.7777 (OUTLIER) cc_final: 0.7408 (m) REVERT: D 56 ASN cc_start: 0.7409 (m-40) cc_final: 0.7121 (m-40) REVERT: D 66 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6593 (pp) outliers start: 53 outliers final: 31 residues processed: 248 average time/residue: 0.2319 time to fit residues: 77.0204 Evaluate side-chains 245 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 208 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 197 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 41 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 25 optimal weight: 0.0670 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.152671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.130835 restraints weight = 12977.324| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.32 r_work: 0.3459 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| r_final: 0.3307 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9022 Z= 0.229 Angle : 0.634 12.761 12226 Z= 0.318 Chirality : 0.044 0.281 1382 Planarity : 0.005 0.091 1544 Dihedral : 5.842 53.366 1264 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.79 % Favored : 94.76 % Rotamer: Outliers : 5.52 % Allowed : 30.49 % Favored : 64.00 % 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: -0.27 (0.25), residues: 1107 helix: 1.15 (0.27), residues: 391 sheet: 0.08 (0.32), residues: 257 loop : -1.52 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 180 HIS 0.003 0.001 HIS A 102 PHE 0.016 0.001 PHE D 95 TYR 0.014 0.001 TYR B 228 ARG 0.008 0.000 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 213 time to evaluate : 0.975 Fit side-chains REVERT: A 38 ASP cc_start: 0.7199 (OUTLIER) cc_final: 0.6978 (p0) REVERT: A 57 ARG cc_start: 0.8332 (ptp-170) cc_final: 0.8093 (ptp-170) REVERT: A 72 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.6746 (mmt) REVERT: A 112 MET cc_start: 0.8023 (ptp) cc_final: 0.7699 (ptp) REVERT: A 129 ASP cc_start: 0.7780 (p0) cc_final: 0.7459 (p0) REVERT: A 135 TYR cc_start: 0.9020 (m-80) cc_final: 0.8593 (m-80) REVERT: A 269 ASP cc_start: 0.7792 (t0) cc_final: 0.7449 (t0) REVERT: B 177 VAL cc_start: 0.8185 (m) cc_final: 0.7937 (p) REVERT: B 179 THR cc_start: 0.8216 (p) cc_final: 0.8002 (t) REVERT: C 17 LYS cc_start: 0.8335 (mttm) cc_final: 0.8078 (mmtm) REVERT: C 189 PHE cc_start: 0.7567 (p90) cc_final: 0.7178 (p90) REVERT: C 197 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7779 (mttm) REVERT: C 200 ASP cc_start: 0.8132 (t0) cc_final: 0.7768 (t0) REVERT: C 245 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6945 (tm-30) REVERT: C 306 GLN cc_start: 0.6359 (mm110) cc_final: 0.5988 (mm110) REVERT: C 316 THR cc_start: 0.7508 (p) cc_final: 0.7218 (t) REVERT: D 18 PHE cc_start: 0.7278 (OUTLIER) cc_final: 0.6940 (p90) REVERT: D 29 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7295 (mt) REVERT: D 52 VAL cc_start: 0.7748 (OUTLIER) cc_final: 0.7372 (m) REVERT: D 56 ASN cc_start: 0.7395 (m-40) cc_final: 0.7146 (m-40) REVERT: D 66 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6606 (pp) REVERT: D 71 ARG cc_start: 0.6985 (ttp80) cc_final: 0.6464 (ttp-110) outliers start: 53 outliers final: 33 residues processed: 242 average time/residue: 0.2463 time to fit residues: 78.8821 Evaluate side-chains 253 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 213 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 290 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 100 optimal weight: 0.5980 chunk 85 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 67 optimal weight: 0.0770 chunk 23 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.151914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.129976 restraints weight = 12849.889| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.28 r_work: 0.3454 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9022 Z= 0.232 Angle : 0.633 14.123 12226 Z= 0.316 Chirality : 0.044 0.255 1382 Planarity : 0.005 0.086 1544 Dihedral : 5.846 52.523 1264 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.97 % Favored : 94.58 % Rotamer: Outliers : 6.66 % Allowed : 29.55 % Favored : 63.79 % 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: -0.32 (0.25), residues: 1107 helix: 1.14 (0.27), residues: 393 sheet: -0.03 (0.31), residues: 264 loop : -1.55 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 140 HIS 0.004 0.001 HIS B 73 PHE 0.017 0.001 PHE A 210 TYR 0.014 0.001 TYR B 228 ARG 0.009 0.001 ARG D 220 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 222 time to evaluate : 0.874 Fit side-chains REVERT: A 38 ASP cc_start: 0.7234 (OUTLIER) cc_final: 0.7024 (p0) REVERT: A 57 ARG cc_start: 0.8316 (ptp-170) cc_final: 0.8014 (ptp-170) REVERT: A 72 MET cc_start: 0.7194 (OUTLIER) cc_final: 0.6753 (mmt) REVERT: A 112 MET cc_start: 0.7933 (ptp) cc_final: 0.7597 (ptp) REVERT: A 135 TYR cc_start: 0.9003 (m-80) cc_final: 0.8594 (m-80) REVERT: A 230 ARG cc_start: 0.7920 (mtm180) cc_final: 0.7437 (mtm180) REVERT: A 269 ASP cc_start: 0.7818 (t0) cc_final: 0.7469 (t0) REVERT: B 179 THR cc_start: 0.8232 (p) cc_final: 0.8025 (t) REVERT: C 17 LYS cc_start: 0.8345 (mttm) cc_final: 0.8100 (mmtm) REVERT: C 189 PHE cc_start: 0.7612 (p90) cc_final: 0.6916 (p90) REVERT: C 200 ASP cc_start: 0.8097 (t0) cc_final: 0.7798 (t0) REVERT: C 245 GLU cc_start: 0.7287 (tm-30) cc_final: 0.6958 (tm-30) REVERT: C 306 GLN cc_start: 0.6398 (mm110) cc_final: 0.6002 (mm110) REVERT: D 18 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.6962 (p90) REVERT: D 29 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7283 (mt) REVERT: D 52 VAL cc_start: 0.7742 (OUTLIER) cc_final: 0.7381 (m) REVERT: D 66 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.6574 (pp) REVERT: D 71 ARG cc_start: 0.7050 (ttp80) cc_final: 0.6778 (ttp-110) REVERT: D 274 LEU cc_start: 0.7766 (tp) cc_final: 0.7153 (tp) REVERT: D 278 PHE cc_start: 0.6779 (p90) cc_final: 0.6461 (p90) outliers start: 64 outliers final: 44 residues processed: 254 average time/residue: 0.2427 time to fit residues: 82.1262 Evaluate side-chains 273 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 223 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain E residue 50 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 103 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 84 optimal weight: 0.2980 chunk 5 optimal weight: 0.0270 chunk 83 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 overall best weight: 0.5240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.152682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.130960 restraints weight = 12812.578| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.25 r_work: 0.3465 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9022 Z= 0.217 Angle : 0.622 14.144 12226 Z= 0.312 Chirality : 0.043 0.245 1382 Planarity : 0.005 0.081 1544 Dihedral : 5.878 54.003 1264 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.06 % Favored : 94.49 % Rotamer: Outliers : 7.28 % Allowed : 28.51 % Favored : 64.20 % 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: -0.33 (0.25), residues: 1107 helix: 1.15 (0.27), residues: 394 sheet: -0.03 (0.31), residues: 258 loop : -1.55 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 140 HIS 0.003 0.001 HIS B 73 PHE 0.016 0.001 PHE A 210 TYR 0.015 0.001 TYR B 141 ARG 0.010 0.001 ARG D 220 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 222 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7270 (OUTLIER) cc_final: 0.7041 (p0) REVERT: A 60 ARG cc_start: 0.7719 (mmp80) cc_final: 0.7110 (tpp-160) REVERT: A 72 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6660 (mmt) REVERT: A 112 MET cc_start: 0.7920 (ptp) cc_final: 0.7586 (ptp) REVERT: A 135 TYR cc_start: 0.8989 (m-80) cc_final: 0.8645 (m-80) REVERT: A 158 SER cc_start: 0.7856 (OUTLIER) cc_final: 0.7339 (p) REVERT: A 223 ASP cc_start: 0.7812 (m-30) cc_final: 0.7603 (m-30) REVERT: A 230 ARG cc_start: 0.7916 (mtm180) cc_final: 0.7432 (mtm180) REVERT: A 245 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.8238 (t80) REVERT: A 269 ASP cc_start: 0.7913 (t0) cc_final: 0.7607 (t0) REVERT: B 155 LEU cc_start: 0.7145 (OUTLIER) cc_final: 0.6790 (tt) REVERT: B 179 THR cc_start: 0.8223 (p) cc_final: 0.7977 (t) REVERT: C 17 LYS cc_start: 0.8343 (mttm) cc_final: 0.8107 (mmtm) REVERT: C 33 GLU cc_start: 0.7426 (tt0) cc_final: 0.7163 (tt0) REVERT: C 197 LYS cc_start: 0.7960 (mttm) cc_final: 0.7479 (mttm) REVERT: C 200 ASP cc_start: 0.8117 (t0) cc_final: 0.7818 (t0) REVERT: C 245 GLU cc_start: 0.7278 (tm-30) cc_final: 0.6908 (tm-30) REVERT: C 317 LYS cc_start: 0.7146 (mtmm) cc_final: 0.6927 (ttmm) REVERT: D 18 PHE cc_start: 0.7331 (OUTLIER) cc_final: 0.7084 (p90) REVERT: D 29 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7279 (mt) REVERT: D 52 VAL cc_start: 0.7761 (OUTLIER) cc_final: 0.7356 (m) REVERT: D 66 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.6547 (pp) REVERT: D 274 LEU cc_start: 0.7872 (tp) cc_final: 0.7262 (tp) REVERT: D 278 PHE cc_start: 0.6812 (p90) cc_final: 0.6444 (p90) outliers start: 70 outliers final: 48 residues processed: 258 average time/residue: 0.2407 time to fit residues: 82.6759 Evaluate side-chains 272 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 215 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain E residue 50 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.0970 chunk 77 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN E 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.150751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.128716 restraints weight = 12927.972| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.28 r_work: 0.3441 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 52 | |-----------------------------------------------------------------------------| r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9022 Z= 0.262 Angle : 0.660 14.237 12226 Z= 0.330 Chirality : 0.044 0.253 1382 Planarity : 0.005 0.079 1544 Dihedral : 5.859 53.651 1262 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.51 % Favored : 94.04 % Rotamer: Outliers : 6.66 % Allowed : 29.76 % Favored : 63.58 % 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: -0.38 (0.25), residues: 1107 helix: 1.10 (0.27), residues: 395 sheet: -0.03 (0.31), residues: 258 loop : -1.60 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 180 HIS 0.004 0.001 HIS B 73 PHE 0.018 0.002 PHE A 210 TYR 0.014 0.002 TYR B 141 ARG 0.017 0.001 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 214 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7387 (OUTLIER) cc_final: 0.7167 (p0) REVERT: A 72 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6699 (mmt) REVERT: A 112 MET cc_start: 0.7955 (ptp) cc_final: 0.7590 (ptp) REVERT: A 135 TYR cc_start: 0.8999 (m-80) cc_final: 0.8627 (m-80) REVERT: A 158 SER cc_start: 0.7883 (OUTLIER) cc_final: 0.7400 (p) REVERT: A 208 ARG cc_start: 0.8386 (tpt-90) cc_final: 0.8156 (tpt-90) REVERT: A 223 ASP cc_start: 0.7834 (m-30) cc_final: 0.7571 (m-30) REVERT: A 230 ARG cc_start: 0.7953 (mtm180) cc_final: 0.7387 (mtm180) REVERT: A 238 SER cc_start: 0.8582 (m) cc_final: 0.8327 (t) REVERT: A 265 ASP cc_start: 0.7496 (t70) cc_final: 0.7121 (t70) REVERT: A 269 ASP cc_start: 0.7932 (t0) cc_final: 0.7576 (t0) REVERT: B 155 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.6918 (tt) REVERT: B 179 THR cc_start: 0.8191 (p) cc_final: 0.7946 (t) REVERT: C 17 LYS cc_start: 0.8335 (mttm) cc_final: 0.8097 (mmtm) REVERT: C 200 ASP cc_start: 0.8128 (t0) cc_final: 0.7834 (t0) REVERT: C 245 GLU cc_start: 0.7304 (tm-30) cc_final: 0.6891 (tm-30) REVERT: C 317 LYS cc_start: 0.7301 (mtmm) cc_final: 0.7060 (ttmm) REVERT: D 18 PHE cc_start: 0.7393 (OUTLIER) cc_final: 0.7134 (p90) REVERT: D 29 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7290 (mt) REVERT: D 52 VAL cc_start: 0.7743 (OUTLIER) cc_final: 0.7360 (m) REVERT: D 59 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7825 (pt) REVERT: D 66 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6651 (pp) outliers start: 64 outliers final: 43 residues processed: 249 average time/residue: 0.2392 time to fit residues: 79.6687 Evaluate side-chains 262 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 210 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 50 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 0.1980 chunk 29 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 98 optimal weight: 0.0970 chunk 95 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.152324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.130359 restraints weight = 13087.336| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.28 r_work: 0.3455 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 52 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 52 | |-----------------------------------------------------------------------------| r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9022 Z= 0.216 Angle : 0.627 14.440 12226 Z= 0.316 Chirality : 0.043 0.196 1382 Planarity : 0.005 0.067 1544 Dihedral : 5.904 55.818 1262 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.97 % Favored : 94.67 % Rotamer: Outliers : 7.08 % Allowed : 29.24 % Favored : 63.68 % 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: -0.34 (0.25), residues: 1107 helix: 1.13 (0.27), residues: 395 sheet: 0.06 (0.31), residues: 258 loop : -1.63 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 180 HIS 0.004 0.001 HIS D 245 PHE 0.039 0.002 PHE D 278 TYR 0.018 0.001 TYR B 273 ARG 0.009 0.000 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 219 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7408 (OUTLIER) cc_final: 0.7176 (p0) REVERT: A 72 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.6712 (mmt) REVERT: A 129 ASP cc_start: 0.7909 (p0) cc_final: 0.7602 (p0) REVERT: A 135 TYR cc_start: 0.8951 (m-80) cc_final: 0.8608 (m-80) REVERT: A 208 ARG cc_start: 0.8368 (tpt-90) cc_final: 0.8130 (tpt-90) REVERT: A 223 ASP cc_start: 0.7922 (m-30) cc_final: 0.7665 (m-30) REVERT: A 230 ARG cc_start: 0.7931 (mtm180) cc_final: 0.7354 (mtm180) REVERT: A 269 ASP cc_start: 0.7930 (t0) cc_final: 0.7591 (t0) REVERT: B 155 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6836 (tt) REVERT: B 179 THR cc_start: 0.8173 (p) cc_final: 0.7931 (t) REVERT: C 17 LYS cc_start: 0.8306 (mttm) cc_final: 0.8059 (mmtm) REVERT: C 33 GLU cc_start: 0.7455 (tt0) cc_final: 0.7096 (tt0) REVERT: C 197 LYS cc_start: 0.7965 (mttm) cc_final: 0.7524 (mttm) REVERT: C 200 ASP cc_start: 0.8122 (t0) cc_final: 0.7817 (t0) REVERT: C 245 GLU cc_start: 0.7347 (tm-30) cc_final: 0.6935 (tm-30) REVERT: C 317 LYS cc_start: 0.7244 (mtmm) cc_final: 0.6997 (ttmm) REVERT: D 18 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.7077 (p90) REVERT: D 29 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7253 (mt) REVERT: D 52 VAL cc_start: 0.7810 (p) cc_final: 0.7425 (m) REVERT: D 59 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7823 (pt) REVERT: D 66 LEU cc_start: 0.6835 (OUTLIER) cc_final: 0.6632 (pp) outliers start: 68 outliers final: 49 residues processed: 257 average time/residue: 0.2395 time to fit residues: 81.3353 Evaluate side-chains 269 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 213 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain E residue 50 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 84 optimal weight: 0.2980 chunk 63 optimal weight: 0.0570 chunk 14 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 23 optimal weight: 0.0870 chunk 3 optimal weight: 0.0470 chunk 15 optimal weight: 0.6980 chunk 74 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.1974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN A 277 HIS D 146 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.154575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.132694 restraints weight = 12991.800| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.29 r_work: 0.3501 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 52 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 52 | |-----------------------------------------------------------------------------| r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9022 Z= 0.163 Angle : 0.606 14.567 12226 Z= 0.305 Chirality : 0.042 0.183 1382 Planarity : 0.005 0.072 1544 Dihedral : 5.902 59.536 1262 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.33 % Favored : 94.40 % Rotamer: Outliers : 5.93 % Allowed : 30.59 % Favored : 63.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.25), residues: 1107 helix: 1.30 (0.27), residues: 389 sheet: 0.14 (0.32), residues: 250 loop : -1.55 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 140 HIS 0.004 0.001 HIS D 245 PHE 0.030 0.001 PHE D 278 TYR 0.015 0.001 TYR B 273 ARG 0.009 0.001 ARG D 220 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 210 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.7050 (p0) REVERT: A 72 MET cc_start: 0.7120 (OUTLIER) cc_final: 0.6604 (mmt) REVERT: A 108 SER cc_start: 0.7807 (t) cc_final: 0.7606 (p) REVERT: A 129 ASP cc_start: 0.7867 (p0) cc_final: 0.7588 (p0) REVERT: A 135 TYR cc_start: 0.8919 (m-80) cc_final: 0.8462 (m-80) REVERT: A 230 ARG cc_start: 0.7889 (mtm180) cc_final: 0.7482 (mtm180) REVERT: A 257 ASP cc_start: 0.7261 (p0) cc_final: 0.7008 (p0) REVERT: A 269 ASP cc_start: 0.7833 (t0) cc_final: 0.7503 (t0) REVERT: B 155 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6739 (tt) REVERT: B 179 THR cc_start: 0.8165 (p) cc_final: 0.7913 (t) REVERT: C 17 LYS cc_start: 0.8258 (mttm) cc_final: 0.8045 (mmtm) REVERT: C 33 GLU cc_start: 0.7358 (tt0) cc_final: 0.7009 (tt0) REVERT: C 197 LYS cc_start: 0.7906 (mttm) cc_final: 0.7521 (mttm) REVERT: C 200 ASP cc_start: 0.8081 (t0) cc_final: 0.7777 (t0) REVERT: C 245 GLU cc_start: 0.7326 (tm-30) cc_final: 0.6943 (tm-30) REVERT: C 277 LYS cc_start: 0.7255 (tttm) cc_final: 0.6925 (tttm) REVERT: C 317 LYS cc_start: 0.6929 (mtmm) cc_final: 0.6506 (mtmt) REVERT: D 18 PHE cc_start: 0.7298 (OUTLIER) cc_final: 0.7055 (p90) REVERT: D 29 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7051 (mt) REVERT: D 52 VAL cc_start: 0.7735 (p) cc_final: 0.7338 (m) REVERT: D 59 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7797 (pt) REVERT: D 115 LEU cc_start: 0.7150 (mt) cc_final: 0.6948 (mm) REVERT: D 220 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.6475 (mpp-170) outliers start: 57 outliers final: 40 residues processed: 244 average time/residue: 0.2376 time to fit residues: 76.7014 Evaluate side-chains 251 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 204 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 4 optimal weight: 0.7980 chunk 100 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.153218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.132874 restraints weight = 13069.625| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.14 r_work: 0.3487 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 52 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| r_final: 0.3328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9022 Z= 0.269 Angle : 0.674 14.495 12226 Z= 0.336 Chirality : 0.045 0.196 1382 Planarity : 0.005 0.074 1544 Dihedral : 5.934 54.757 1262 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.69 % Favored : 93.95 % Rotamer: Outliers : 5.10 % Allowed : 31.53 % Favored : 63.37 % 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: -0.33 (0.25), residues: 1107 helix: 1.19 (0.26), residues: 392 sheet: -0.10 (0.31), residues: 256 loop : -1.54 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 180 HIS 0.004 0.001 HIS B 73 PHE 0.032 0.002 PHE D 278 TYR 0.016 0.002 TYR A 96 ARG 0.008 0.001 ARG D 292 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 216 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.7203 (p0) REVERT: A 129 ASP cc_start: 0.7802 (p0) cc_final: 0.7559 (p0) REVERT: A 135 TYR cc_start: 0.8918 (m-80) cc_final: 0.8538 (m-80) REVERT: A 208 ARG cc_start: 0.8285 (tpt-90) cc_final: 0.8026 (tpt-90) REVERT: A 230 ARG cc_start: 0.7935 (mtm180) cc_final: 0.7526 (mtm180) REVERT: A 269 ASP cc_start: 0.7939 (t0) cc_final: 0.7541 (t0) REVERT: B 155 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.6995 (tt) REVERT: B 179 THR cc_start: 0.8179 (p) cc_final: 0.7936 (t) REVERT: C 17 LYS cc_start: 0.8382 (mttm) cc_final: 0.8173 (mmtm) REVERT: C 199 PHE cc_start: 0.8091 (m-80) cc_final: 0.7563 (m-80) REVERT: C 200 ASP cc_start: 0.8069 (t0) cc_final: 0.7748 (t0) REVERT: C 245 GLU cc_start: 0.7384 (tm-30) cc_final: 0.7064 (tm-30) REVERT: C 317 LYS cc_start: 0.7470 (mtmm) cc_final: 0.7164 (ttmt) REVERT: D 18 PHE cc_start: 0.7368 (OUTLIER) cc_final: 0.7097 (p90) REVERT: D 29 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7351 (mt) REVERT: D 52 VAL cc_start: 0.7721 (p) cc_final: 0.7347 (m) REVERT: D 59 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7788 (pt) outliers start: 49 outliers final: 41 residues processed: 246 average time/residue: 0.2352 time to fit residues: 77.3383 Evaluate side-chains 259 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 213 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 92 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN C 294 ASN C 322 HIS C 331 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.150335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.129557 restraints weight = 13049.379| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.17 r_work: 0.3456 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3302 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9022 Z= 0.307 Angle : 0.700 14.910 12226 Z= 0.349 Chirality : 0.046 0.196 1382 Planarity : 0.005 0.075 1544 Dihedral : 6.142 55.666 1262 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.23 % Favored : 93.41 % Rotamer: Outliers : 5.20 % Allowed : 31.63 % Favored : 63.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.25), residues: 1107 helix: 1.03 (0.26), residues: 393 sheet: -0.17 (0.32), residues: 250 loop : -1.61 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 180 HIS 0.004 0.001 HIS B 73 PHE 0.030 0.002 PHE D 278 TYR 0.022 0.002 TYR B 98 ARG 0.008 0.001 ARG D 220 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5442.90 seconds wall clock time: 97 minutes 5.51 seconds (5825.51 seconds total)