Starting phenix.real_space_refine on Thu Jul 2 15:34:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8t3o_41007/07_2026/8t3o_41007.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t3o_41007/07_2026/8t3o_41007.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t3o_41007/07_2026/8t3o_41007.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t3o_41007/07_2026/8t3o_41007.map" model { file = "/net/cci-nas-00/data/ceres_data/8t3o_41007/07_2026/8t3o_41007.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t3o_41007/07_2026/8t3o_41007.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8t3o_41007/07_2026/8t3o_41007.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8t3o_41007/07_2026/8t3o_41007.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.035 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 55 5.16 5 C 5810 2.51 5 N 1561 2.21 5 O 1680 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9109 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2363 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 12, 'TRANS': 284} Chain breaks: 2 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "A" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1797 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 4, 'PHE:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 49 Chain: "N" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1781 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 110 Unusual residues: {'2Y5': 1, 'PLM': 1, 'YN9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.92, per 1000 atoms: 0.21 Number of scatterers: 9109 At special positions: 0 Unit cell: (86.112, 122.544, 127.512, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 55 16.00 P 2 15.00 F 1 9.00 O 1680 8.00 N 1561 7.00 C 5810 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 111 " - pdb=" SG CYS R 194 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 160 " - pdb=" SG CYS N 230 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 242.7 milliseconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 16 sheets defined 36.9% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'R' and resid 35 through 71 removed outlier: 4.193A pdb=" N ALA R 41 " --> pdb=" O LEU R 37 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL R 42 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU R 47 " --> pdb=" O GLU R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 89 removed outlier: 3.626A pdb=" N LEU R 81 " --> pdb=" O LEU R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 102 removed outlier: 3.702A pdb=" N VAL R 95 " --> pdb=" O ALA R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 142 removed outlier: 3.788A pdb=" N CYS R 111 " --> pdb=" O GLY R 107 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE R 115 " --> pdb=" O CYS R 111 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N TYR R 116 " --> pdb=" O HIS R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 176 Proline residue: R 172 - end of helix removed outlier: 3.755A pdb=" N PHE R 176 " --> pdb=" O PRO R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 200 through 214 Processing helix chain 'R' and resid 216 through 244 removed outlier: 3.524A pdb=" N LEU R 231 " --> pdb=" O TYR R 227 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR R 242 " --> pdb=" O ARG R 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 256 Processing helix chain 'R' and resid 257 through 277 removed outlier: 4.009A pdb=" N ARG R 261 " --> pdb=" O GLN R 257 " (cutoff:3.500A) Processing helix chain 'R' and resid 278 through 291 removed outlier: 3.781A pdb=" N ASN R 291 " --> pdb=" O ILE R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 321 removed outlier: 3.725A pdb=" N SER R 314 " --> pdb=" O THR R 310 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA R 315 " --> pdb=" O PHE R 311 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU R 316 " --> pdb=" O ALA R 312 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN R 317 " --> pdb=" O ASN R 313 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.603A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.695A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.699A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.949A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 102 removed outlier: 4.458A pdb=" N ASP A 102 " --> pdb=" O CYS A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.575A pdb=" N ARG A 135 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.581A pdb=" N LEU A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.453A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 removed outlier: 4.340A pdb=" N ARG A 169 " --> pdb=" O PRO A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 203 Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.914A pdb=" N THR N 91 " --> pdb=" O SER N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 177 through 181 removed outlier: 3.551A pdb=" N ARG R 178 " --> pdb=" O THR R 195 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR R 195 " --> pdb=" O ARG R 178 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL R 180 " --> pdb=" O ILE R 193 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE R 193 " --> pdb=" O VAL R 180 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51 removed outlier: 3.676A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.580A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.936A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.298A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.926A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.412A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.374A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 34 through 35 removed outlier: 6.297A pdb=" N LEU A 34 " --> pdb=" O HIS A 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 38 through 39 removed outlier: 6.316A pdb=" N LEU A 39 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ASP A 111 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 38 through 39 removed outlier: 6.316A pdb=" N LEU A 39 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ASP A 111 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.833A pdb=" N MET N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TYR N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 11 through 12 removed outlier: 4.201A pdb=" N PHE N 110 " --> pdb=" O ARG N 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 141 through 143 Processing sheet with id=AB7, first strand: chain 'N' and resid 147 through 149 removed outlier: 6.546A pdb=" N LEU N 175 " --> pdb=" O TYR N 191 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N TYR N 191 " --> pdb=" O LEU N 175 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP N 177 " --> pdb=" O LEU N 189 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1248 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.27 Time building geometry restraints manager: 1.22 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: 1455 1.31 - 1.44: 2570 1.44 - 1.56: 5186 1.56 - 1.69: 4 1.69 - 1.81: 79 Bond restraints: 9294 Sorted by residual: bond pdb=" C1 YN9 R 401 " pdb=" C3 YN9 R 401 " ideal model delta sigma weight residual 1.481 1.380 0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" CA SER B 331 " pdb=" CB SER B 331 " ideal model delta sigma weight residual 1.532 1.471 0.061 1.68e-02 3.54e+03 1.31e+01 bond pdb=" N VAL A 50 " pdb=" CA VAL A 50 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.25e-02 6.40e+03 1.18e+01 bond pdb=" N CYS R 194 " pdb=" CA CYS R 194 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.19e-02 7.06e+03 1.15e+01 bond pdb=" C10 2Y5 R 402 " pdb=" O16 2Y5 R 402 " ideal model delta sigma weight residual 1.333 1.399 -0.066 2.00e-02 2.50e+03 1.08e+01 ... (remaining 9289 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 12276 2.63 - 5.25: 279 5.25 - 7.88: 38 7.88 - 10.50: 4 10.50 - 13.13: 2 Bond angle restraints: 12599 Sorted by residual: angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.47 106.96 6.51 1.01e+00 9.80e-01 4.15e+01 angle pdb=" CA GLY N 33 " pdb=" C GLY N 33 " pdb=" O GLY N 33 " ideal model delta sigma weight residual 121.41 117.03 4.38 8.80e-01 1.29e+00 2.47e+01 angle pdb=" CA GLY B 41 " pdb=" C GLY B 41 " pdb=" O GLY B 41 " ideal model delta sigma weight residual 122.57 118.24 4.33 9.20e-01 1.18e+00 2.21e+01 angle pdb=" C ASP A 199 " pdb=" CA ASP A 199 " pdb=" CB ASP A 199 " ideal model delta sigma weight residual 110.88 103.55 7.33 1.57e+00 4.06e-01 2.18e+01 angle pdb=" N MET N 193 " pdb=" CA MET N 193 " pdb=" CB MET N 193 " ideal model delta sigma weight residual 114.17 108.85 5.32 1.14e+00 7.69e-01 2.17e+01 ... (remaining 12594 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.85: 5304 31.85 - 63.70: 229 63.70 - 95.56: 23 95.56 - 127.41: 7 127.41 - 159.26: 1 Dihedral angle restraints: 5564 sinusoidal: 2209 harmonic: 3355 Sorted by residual: dihedral pdb=" CB CYS R 111 " pdb=" SG CYS R 111 " pdb=" SG CYS R 194 " pdb=" CB CYS R 194 " ideal model delta sinusoidal sigma weight residual -86.00 -148.52 62.52 1 1.00e+01 1.00e-02 5.17e+01 dihedral pdb=" C16 2Y5 R 402 " pdb=" C17 2Y5 R 402 " pdb=" C18 2Y5 R 402 " pdb=" C19 2Y5 R 402 " ideal model delta sinusoidal sigma weight residual 249.33 90.07 159.26 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" C8 YN9 R 401 " pdb=" C2 YN9 R 401 " pdb=" C4 YN9 R 401 " pdb=" O1 YN9 R 401 " ideal model delta sinusoidal sigma weight residual -88.00 30.92 -118.92 1 3.00e+01 1.11e-03 1.58e+01 ... (remaining 5561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.003: 1443 1.003 - 2.006: 0 2.006 - 3.009: 0 3.009 - 4.012: 0 4.012 - 5.015: 1 Chirality restraints: 1444 Sorted by residual: chirality pdb=" C1 2Y5 R 402 " pdb=" C2 2Y5 R 402 " pdb=" C6 2Y5 R 402 " pdb=" O1 2Y5 R 402 " both_signs ideal model delta sigma weight residual False -2.53 2.48 -5.02 2.00e-01 2.50e+01 6.29e+02 chirality pdb=" CA ILE A 200 " pdb=" N ILE A 200 " pdb=" C ILE A 200 " pdb=" CB ILE A 200 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 1441 not shown) Planarity restraints: 1590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 312 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" CG ASP B 312 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASP B 312 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP B 312 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 171 " -0.035 5.00e-02 4.00e+02 5.31e-02 4.51e+00 pdb=" N PRO R 172 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO R 172 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO R 172 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG N 192 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C ARG N 192 " -0.033 2.00e-02 2.50e+03 pdb=" O ARG N 192 " 0.012 2.00e-02 2.50e+03 pdb=" N MET N 193 " 0.012 2.00e-02 2.50e+03 ... (remaining 1587 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 208 2.68 - 3.23: 8677 3.23 - 3.79: 14552 3.79 - 4.34: 19556 4.34 - 4.90: 33154 Nonbonded interactions: 76147 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.123 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.192 3.040 nonbonded pdb=" OG1 THR R 242 " pdb=" OE1 GLN R 252 " model vdw 2.201 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.203 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR N 176 " model vdw 2.216 3.040 ... (remaining 76142 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 8.650 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 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 0.101 9297 Z= 0.354 Angle : 0.881 13.128 12605 Z= 0.530 Chirality : 0.142 5.015 1444 Planarity : 0.004 0.053 1590 Dihedral : 17.725 159.259 3383 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.21 % Allowed : 22.94 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.25), residues: 1140 helix: 1.23 (0.28), residues: 366 sheet: -0.28 (0.31), residues: 275 loop : -0.09 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 32 TYR 0.015 0.001 TYR N 191 PHE 0.025 0.002 PHE R 267 TRP 0.021 0.002 TRP R 104 HIS 0.003 0.001 HIS R 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.35 ( 9294) covalent geometry : angle 0.88057 / 0.53 (12599) SS BOND : bond 0.00804 / 0.42 ( 3) SS BOND : angle 1.44270 / 0.77 ( 6) hydrogen bonds : bond 0.17111 / 11.77 ( 433) hydrogen bonds : angle 6.86190 / 5.06 ( 1248) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 131 average time/residue: 0.0968 time to fit residues: 16.7169 Evaluate side-chains 119 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 177 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 ASN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN A 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.161196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.113553 restraints weight = 10818.192| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.65 r_work: 0.3173 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9297 Z= 0.201 Angle : 0.592 7.511 12605 Z= 0.308 Chirality : 0.044 0.202 1444 Planarity : 0.004 0.055 1590 Dihedral : 11.252 157.297 1369 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.98 % Allowed : 22.33 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.25), residues: 1140 helix: 1.30 (0.26), residues: 373 sheet: -0.32 (0.31), residues: 279 loop : -0.05 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 32 TYR 0.014 0.002 TYR N 191 PHE 0.020 0.002 PHE N 68 TRP 0.013 0.002 TRP R 104 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 ( 9294) covalent geometry : angle 0.59119 / 0.31 (12599) SS BOND : bond 0.00419 / 0.21 ( 3) SS BOND : angle 1.06052 / 0.55 ( 6) hydrogen bonds : bond 0.04583 / 3.10 ( 433) hydrogen bonds : angle 5.00969 / 3.68 ( 1248) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: R 105 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8060 (pp) REVERT: A 166 GLU cc_start: 0.7191 (tp30) cc_final: 0.6961 (tp30) REVERT: N 11 LEU cc_start: 0.7785 (tp) cc_final: 0.7318 (mm) REVERT: N 142 THR cc_start: 0.8452 (m) cc_final: 0.8144 (p) outliers start: 29 outliers final: 15 residues processed: 150 average time/residue: 0.1033 time to fit residues: 20.7507 Evaluate side-chains 137 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 177 PHE Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 171 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 59 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.156998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.109920 restraints weight = 10771.468| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.59 r_work: 0.3144 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 9297 Z= 0.263 Angle : 0.629 8.021 12605 Z= 0.326 Chirality : 0.045 0.170 1444 Planarity : 0.004 0.054 1590 Dihedral : 10.297 157.148 1369 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.25 % Allowed : 21.60 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.25), residues: 1140 helix: 1.26 (0.26), residues: 374 sheet: -0.38 (0.30), residues: 285 loop : -0.11 (0.30), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 36 TYR 0.012 0.002 TYR R 321 PHE 0.016 0.002 PHE N 68 TRP 0.015 0.002 TRP R 104 HIS 0.004 0.001 HIS N 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.26 ( 9294) covalent geometry : angle 0.62883 / 0.33 (12599) SS BOND : bond 0.00553 / 0.28 ( 3) SS BOND : angle 1.15023 / 0.58 ( 6) hydrogen bonds : bond 0.04703 / 3.19 ( 433) hydrogen bonds : angle 5.03127 / 3.70 ( 1248) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 120 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: R 105 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7947 (pp) REVERT: A 166 GLU cc_start: 0.7249 (tp30) cc_final: 0.6999 (tp30) REVERT: N 11 LEU cc_start: 0.7829 (tp) cc_final: 0.7315 (mm) REVERT: N 83 MET cc_start: 0.8768 (mtp) cc_final: 0.8499 (mtp) REVERT: N 142 THR cc_start: 0.8482 (m) cc_final: 0.8205 (p) outliers start: 51 outliers final: 32 residues processed: 154 average time/residue: 0.0929 time to fit residues: 19.2127 Evaluate side-chains 148 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 166 SER Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 265 THR Chi-restraints excluded: chain R residue 275 ILE Chi-restraints excluded: chain R residue 313 ASN Chi-restraints excluded: chain R residue 319 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain N residue 215 LEU Chi-restraints excluded: chain N residue 227 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 9 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 100 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN A 131 ASN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.159149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.111826 restraints weight = 10857.015| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.63 r_work: 0.3172 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9297 Z= 0.187 Angle : 0.576 9.171 12605 Z= 0.294 Chirality : 0.043 0.146 1444 Planarity : 0.004 0.054 1590 Dihedral : 8.989 152.562 1367 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 5.04 % Allowed : 21.71 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.25), residues: 1140 helix: 1.43 (0.26), residues: 376 sheet: -0.38 (0.31), residues: 284 loop : -0.12 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.014 0.001 TYR N 191 PHE 0.013 0.002 PHE N 68 TRP 0.014 0.002 TRP R 104 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 ( 9294) covalent geometry : angle 0.57626 / 0.29 (12599) SS BOND : bond 0.00630 / 0.33 ( 3) SS BOND : angle 0.76013 / 0.39 ( 6) hydrogen bonds : bond 0.04156 / 2.82 ( 433) hydrogen bonds : angle 4.79540 / 3.52 ( 1248) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 124 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: R 105 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7832 (pp) REVERT: B 219 ARG cc_start: 0.7860 (mtp85) cc_final: 0.7575 (mtp85) REVERT: G 62 ARG cc_start: 0.6632 (ptp90) cc_final: 0.6334 (ptp90) REVERT: A 166 GLU cc_start: 0.7334 (tp30) cc_final: 0.7069 (tp30) REVERT: N 11 LEU cc_start: 0.7875 (tp) cc_final: 0.7323 (mm) REVERT: N 142 THR cc_start: 0.8455 (m) cc_final: 0.8229 (p) outliers start: 49 outliers final: 35 residues processed: 160 average time/residue: 0.0876 time to fit residues: 19.0576 Evaluate side-chains 155 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 222 VAL Chi-restraints excluded: chain R residue 265 THR Chi-restraints excluded: chain R residue 272 SER Chi-restraints excluded: chain R residue 275 ILE Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 313 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain N residue 215 LEU Chi-restraints excluded: chain N residue 227 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 61 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 313 ASN B 44 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.161980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.117169 restraints weight = 10756.952| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.61 r_work: 0.3239 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9297 Z= 0.117 Angle : 0.533 8.396 12605 Z= 0.269 Chirality : 0.041 0.145 1444 Planarity : 0.004 0.051 1590 Dihedral : 8.141 147.765 1367 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.42 % Allowed : 22.94 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.26), residues: 1140 helix: 1.83 (0.26), residues: 370 sheet: -0.30 (0.31), residues: 276 loop : -0.12 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 19 TYR 0.015 0.001 TYR N 191 PHE 0.022 0.001 PHE R 51 TRP 0.012 0.001 TRP B 169 HIS 0.002 0.001 HIS N 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 9294) covalent geometry : angle 0.53336 / 0.27 (12599) SS BOND : bond 0.00536 / 0.27 ( 3) SS BOND : angle 0.64419 / 0.33 ( 6) hydrogen bonds : bond 0.03642 / 2.49 ( 433) hydrogen bonds : angle 4.52537 / 3.31 ( 1248) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 132 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 105 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7776 (pp) REVERT: B 219 ARG cc_start: 0.7713 (mtp85) cc_final: 0.7380 (mtp85) REVERT: B 312 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.8221 (t0) REVERT: A 117 ARG cc_start: 0.7388 (ptm160) cc_final: 0.7143 (ptm160) REVERT: A 166 GLU cc_start: 0.7331 (tp30) cc_final: 0.7103 (tp30) REVERT: N 11 LEU cc_start: 0.7862 (tp) cc_final: 0.7339 (mm) REVERT: N 18 ARG cc_start: 0.8142 (tpp-160) cc_final: 0.7637 (tpt-90) REVERT: N 83 MET cc_start: 0.8503 (mtt) cc_final: 0.8100 (mtp) REVERT: N 142 THR cc_start: 0.8400 (m) cc_final: 0.8185 (p) outliers start: 43 outliers final: 32 residues processed: 164 average time/residue: 0.0914 time to fit residues: 20.2692 Evaluate side-chains 158 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 222 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 319 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 227 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 11 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 0.1980 chunk 17 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 16 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.162860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.115751 restraints weight = 10873.722| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.65 r_work: 0.3207 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9297 Z= 0.141 Angle : 0.542 7.357 12605 Z= 0.275 Chirality : 0.041 0.137 1444 Planarity : 0.004 0.050 1590 Dihedral : 8.055 145.890 1367 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.32 % Allowed : 23.35 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.26), residues: 1140 helix: 1.79 (0.27), residues: 376 sheet: -0.30 (0.31), residues: 274 loop : -0.14 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 19 TYR 0.013 0.001 TYR N 191 PHE 0.021 0.001 PHE N 68 TRP 0.013 0.001 TRP R 104 HIS 0.003 0.001 HIS N 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 9294) covalent geometry : angle 0.54228 / 0.27 (12599) SS BOND : bond 0.00493 / 0.25 ( 3) SS BOND : angle 0.88365 / 0.45 ( 6) hydrogen bonds : bond 0.03741 / 2.55 ( 433) hydrogen bonds : angle 4.49998 / 3.30 ( 1248) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 131 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 105 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7748 (pp) REVERT: B 32 GLN cc_start: 0.8602 (mt0) cc_final: 0.8382 (mt0) REVERT: B 219 ARG cc_start: 0.7751 (mtp85) cc_final: 0.7428 (mtp85) REVERT: B 312 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8187 (t0) REVERT: G 62 ARG cc_start: 0.6637 (ptp90) cc_final: 0.5954 (ptp90) REVERT: A 166 GLU cc_start: 0.7480 (tp30) cc_final: 0.7234 (tp30) REVERT: N 11 LEU cc_start: 0.7903 (tp) cc_final: 0.7367 (mm) REVERT: N 18 ARG cc_start: 0.8152 (tpp-160) cc_final: 0.7663 (tpt-90) REVERT: N 142 THR cc_start: 0.8441 (m) cc_final: 0.8239 (p) outliers start: 42 outliers final: 36 residues processed: 162 average time/residue: 0.0934 time to fit residues: 20.2537 Evaluate side-chains 163 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 115 PHE Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 222 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 275 ILE Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 319 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 215 LEU Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 227 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 34 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 112 optimal weight: 0.5980 chunk 82 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 258 GLN ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.162002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.117130 restraints weight = 10803.627| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.62 r_work: 0.3242 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9297 Z= 0.121 Angle : 0.534 11.030 12605 Z= 0.267 Chirality : 0.041 0.183 1444 Planarity : 0.004 0.068 1590 Dihedral : 7.830 142.358 1367 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 5.04 % Allowed : 22.63 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.26), residues: 1140 helix: 1.92 (0.27), residues: 376 sheet: -0.30 (0.32), residues: 274 loop : -0.14 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 19 TYR 0.013 0.001 TYR N 191 PHE 0.018 0.001 PHE R 51 TRP 0.011 0.001 TRP B 169 HIS 0.002 0.001 HIS N 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 9294) covalent geometry : angle 0.53368 / 0.27 (12599) SS BOND : bond 0.00458 / 0.24 ( 3) SS BOND : angle 0.84387 / 0.42 ( 6) hydrogen bonds : bond 0.03555 / 2.43 ( 433) hydrogen bonds : angle 4.39280 / 3.22 ( 1248) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 126 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 219 ARG cc_start: 0.7697 (mtp85) cc_final: 0.7372 (mtp85) REVERT: B 312 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.8152 (t0) REVERT: G 62 ARG cc_start: 0.6527 (ptp90) cc_final: 0.6308 (ptp90) REVERT: A 166 GLU cc_start: 0.7433 (tp30) cc_final: 0.7152 (tp30) REVERT: N 11 LEU cc_start: 0.7888 (tp) cc_final: 0.7353 (mm) REVERT: N 18 ARG cc_start: 0.8112 (tpp-160) cc_final: 0.7606 (tpt-90) REVERT: N 93 MET cc_start: 0.7844 (tpp) cc_final: 0.7452 (tpp) REVERT: N 142 THR cc_start: 0.8361 (m) cc_final: 0.8157 (p) REVERT: N 161 ARG cc_start: 0.6911 (ttp80) cc_final: 0.6708 (mtp-110) outliers start: 49 outliers final: 40 residues processed: 163 average time/residue: 0.0926 time to fit residues: 20.3073 Evaluate side-chains 166 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 222 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 272 SER Chi-restraints excluded: chain R residue 275 ILE Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 215 LEU Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 227 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 42 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.157557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.112321 restraints weight = 10763.922| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.58 r_work: 0.3179 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 9297 Z= 0.233 Angle : 0.614 9.807 12605 Z= 0.311 Chirality : 0.044 0.157 1444 Planarity : 0.004 0.063 1590 Dihedral : 8.178 142.247 1367 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.14 % Allowed : 22.63 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.25), residues: 1140 helix: 1.65 (0.26), residues: 379 sheet: -0.37 (0.31), residues: 279 loop : -0.20 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 36 TYR 0.013 0.002 TYR R 321 PHE 0.025 0.002 PHE N 68 TRP 0.012 0.002 TRP B 297 HIS 0.004 0.001 HIS N 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.23 ( 9294) covalent geometry : angle 0.61377 / 0.31 (12599) SS BOND : bond 0.00450 / 0.23 ( 3) SS BOND : angle 1.19754 / 0.59 ( 6) hydrogen bonds : bond 0.04194 / 2.86 ( 433) hydrogen bonds : angle 4.68087 / 3.45 ( 1248) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 126 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: B 312 ASP cc_start: 0.8650 (OUTLIER) cc_final: 0.8394 (t0) REVERT: G 62 ARG cc_start: 0.6416 (ptp90) cc_final: 0.6150 (ptp90) REVERT: A 166 GLU cc_start: 0.7378 (tp30) cc_final: 0.7163 (tp30) REVERT: N 11 LEU cc_start: 0.7829 (tp) cc_final: 0.7291 (mm) REVERT: N 18 ARG cc_start: 0.8032 (tpp-160) cc_final: 0.7447 (tpt-90) REVERT: N 83 MET cc_start: 0.8579 (mtt) cc_final: 0.8323 (mtp) REVERT: N 93 MET cc_start: 0.7806 (tpp) cc_final: 0.7333 (tpp) REVERT: N 142 THR cc_start: 0.8357 (m) cc_final: 0.8110 (p) outliers start: 50 outliers final: 39 residues processed: 163 average time/residue: 0.0811 time to fit residues: 18.0295 Evaluate side-chains 167 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 127 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 115 PHE Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 222 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 272 SER Chi-restraints excluded: chain R residue 275 ILE Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 319 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 215 LEU Chi-restraints excluded: chain N residue 216 THR Chi-restraints excluded: chain N residue 227 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 6 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN A 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.162921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.118180 restraints weight = 10740.660| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.61 r_work: 0.3249 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9297 Z= 0.112 Angle : 0.548 9.860 12605 Z= 0.271 Chirality : 0.041 0.148 1444 Planarity : 0.004 0.056 1590 Dihedral : 7.674 137.300 1367 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.12 % Allowed : 23.77 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.26), residues: 1140 helix: 1.88 (0.26), residues: 382 sheet: -0.35 (0.32), residues: 274 loop : -0.16 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 19 TYR 0.015 0.001 TYR N 191 PHE 0.016 0.001 PHE R 51 TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS R 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 9294) covalent geometry : angle 0.54787 / 0.27 (12599) SS BOND : bond 0.00485 / 0.25 ( 3) SS BOND : angle 0.71486 / 0.37 ( 6) hydrogen bonds : bond 0.03464 / 2.39 ( 433) hydrogen bonds : angle 4.41990 / 3.24 ( 1248) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 125 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: B 219 ARG cc_start: 0.7725 (mtp85) cc_final: 0.7494 (mtp85) REVERT: B 312 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.8160 (t0) REVERT: G 62 ARG cc_start: 0.6577 (ptp90) cc_final: 0.6354 (ptp90) REVERT: A 166 GLU cc_start: 0.7433 (tp30) cc_final: 0.7156 (tp30) REVERT: N 11 LEU cc_start: 0.7846 (tp) cc_final: 0.7321 (mm) REVERT: N 18 ARG cc_start: 0.8122 (tpp-160) cc_final: 0.7512 (tpt-90) REVERT: N 76 LYS cc_start: 0.8394 (mtpp) cc_final: 0.8184 (mtmm) REVERT: N 83 MET cc_start: 0.8561 (mtt) cc_final: 0.8193 (mtp) REVERT: N 142 THR cc_start: 0.8347 (m) cc_final: 0.8146 (p) outliers start: 40 outliers final: 36 residues processed: 157 average time/residue: 0.0830 time to fit residues: 17.7054 Evaluate side-chains 160 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 115 PHE Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 222 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 272 SER Chi-restraints excluded: chain R residue 275 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 216 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 113 optimal weight: 20.0000 chunk 100 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 80 ASN ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 ASN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.162677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.118104 restraints weight = 10721.657| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.62 r_work: 0.3248 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.187 9297 Z= 0.166 Angle : 0.871 59.192 12605 Z= 0.504 Chirality : 0.044 0.573 1444 Planarity : 0.004 0.053 1590 Dihedral : 7.717 137.254 1367 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.22 % Allowed : 23.66 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.26), residues: 1140 helix: 1.89 (0.26), residues: 382 sheet: -0.35 (0.32), residues: 274 loop : -0.16 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 19 TYR 0.014 0.001 TYR N 191 PHE 0.015 0.001 PHE R 51 TRP 0.012 0.001 TRP B 169 HIS 0.002 0.001 HIS R 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 ( 9294) covalent geometry : angle 0.87116 / 0.50 (12599) SS BOND : bond 0.00497 / 0.25 ( 3) SS BOND : angle 0.75812 / 0.40 ( 6) hydrogen bonds : bond 0.03507 / 2.42 ( 433) hydrogen bonds : angle 4.42102 / 3.24 ( 1248) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: B 219 ARG cc_start: 0.7731 (mtp85) cc_final: 0.7495 (mtp85) REVERT: B 312 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8161 (t0) REVERT: G 62 ARG cc_start: 0.6569 (ptp90) cc_final: 0.6345 (ptp90) REVERT: A 166 GLU cc_start: 0.7431 (tp30) cc_final: 0.7152 (tp30) REVERT: N 11 LEU cc_start: 0.7849 (tp) cc_final: 0.7325 (mm) REVERT: N 18 ARG cc_start: 0.8101 (tpp-160) cc_final: 0.7511 (tpt-90) REVERT: N 76 LYS cc_start: 0.8392 (mtpp) cc_final: 0.8181 (mtmm) REVERT: N 83 MET cc_start: 0.8458 (mtt) cc_final: 0.8193 (mtp) outliers start: 41 outliers final: 36 residues processed: 154 average time/residue: 0.1084 time to fit residues: 22.2342 Evaluate side-chains 158 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 121 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 115 PHE Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 222 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 272 SER Chi-restraints excluded: chain R residue 275 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 216 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 63 optimal weight: 0.0670 chunk 66 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 90 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.162590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118181 restraints weight = 10684.644| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.58 r_work: 0.3251 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.187 9297 Z= 0.166 Angle : 0.871 59.192 12605 Z= 0.504 Chirality : 0.044 0.573 1444 Planarity : 0.004 0.053 1590 Dihedral : 7.717 137.254 1367 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.91 % Allowed : 23.97 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.26), residues: 1140 helix: 1.89 (0.26), residues: 382 sheet: -0.35 (0.32), residues: 274 loop : -0.16 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 19 TYR 0.014 0.001 TYR N 191 PHE 0.015 0.001 PHE R 51 TRP 0.012 0.001 TRP B 169 HIS 0.002 0.001 HIS R 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 ( 9294) covalent geometry : angle 0.87117 / 0.50 (12599) SS BOND : bond 0.00497 / 0.25 ( 3) SS BOND : angle 0.75812 / 0.40 ( 6) hydrogen bonds : bond 0.03507 / 2.42 ( 433) hydrogen bonds : angle 4.42102 / 3.24 ( 1248) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1853.72 seconds wall clock time: 32 minutes 38.36 seconds (1958.36 seconds total)