Starting phenix.real_space_refine on Sat May 2 17:57:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9itb_60857/05_2026/9itb_60857.cif Found real_map, /net/cci-nas-00/data/ceres_data/9itb_60857/05_2026/9itb_60857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9itb_60857/05_2026/9itb_60857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9itb_60857/05_2026/9itb_60857.map" model { file = "/net/cci-nas-00/data/ceres_data/9itb_60857/05_2026/9itb_60857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9itb_60857/05_2026/9itb_60857.cif" } resolution = 2.89 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= 0.041 sd= 0.148 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 61 5.16 5 C 5127 2.51 5 N 1320 2.21 5 O 1471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7980 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1818 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2514 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 45 Chain: "N" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 963 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "R" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2147 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 10, 'TRANS': 260} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 30 Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 407 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "R" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 131 Unusual residues: {'CLR': 3, 'NKP': 1, 'PLM': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 2.00, per 1000 atoms: 0.25 Number of scatterers: 7980 At special positions: 0 Unit cell: (72.6, 101.2, 135.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 61 16.00 P 1 15.00 O 1471 8.00 N 1320 7.00 C 5127 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 9 " - pdb=" SG CYS R 263 " distance=2.03 Simple disulfide: pdb=" SG CYS R 89 " - pdb=" SG CYS R 168 " 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: 0.59 Conformation dependent library (CDL) restraints added in 396.9 milliseconds 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1924 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 40.7% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 15 through 38 removed outlier: 3.703A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 58 Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.503A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.515A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.713A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.518A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.935A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.615A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 15 through 45 removed outlier: 4.373A pdb=" N GLY R 21 " --> pdb=" O TYR R 17 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER R 25 " --> pdb=" O GLY R 21 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N MET R 26 " --> pdb=" O CYS R 22 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU R 32 " --> pdb=" O PHE R 28 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE R 33 " --> pdb=" O VAL R 29 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N CYS R 36 " --> pdb=" O LEU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 68 Processing helix chain 'R' and resid 69 through 80 removed outlier: 4.533A pdb=" N ARG R 73 " --> pdb=" O THR R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 120 removed outlier: 4.164A pdb=" N CYS R 89 " --> pdb=" O GLY R 85 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE R 104 " --> pdb=" O MET R 100 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR R 120 " --> pdb=" O LEU R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 146 Processing helix chain 'R' and resid 148 through 153 Processing helix chain 'R' and resid 173 through 180 removed outlier: 3.682A pdb=" N TRP R 177 " --> pdb=" O PRO R 173 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR R 179 " --> pdb=" O ALA R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 193 removed outlier: 3.750A pdb=" N ILE R 184 " --> pdb=" O TYR R 180 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE R 193 " --> pdb=" O GLU R 189 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 210 Processing helix chain 'R' and resid 227 through 258 removed outlier: 4.363A pdb=" N ILE R 231 " --> pdb=" O VAL R 227 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE R 232 " --> pdb=" O LEU R 228 " (cutoff:3.500A) Proline residue: R 244 - end of helix Processing helix chain 'R' and resid 262 through 276 Proline residue: R 274 - end of helix Processing helix chain 'R' and resid 277 through 283 removed outlier: 3.671A pdb=" N VAL R 281 " --> pdb=" O LEU R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 286 through 291 Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.543A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 4.008A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.578A pdb=" N GLU G 58 " --> pdb=" O PRO G 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.302A pdb=" N LEU A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N PHE A 222 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.832A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.718A 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: 6.987A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.755A 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: 6.895A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.699A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.564A 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: 6.997A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.893A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.617A 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: 6.474A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.172A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 377 hydrogen bonds defined for protein. 1071 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: 0.89 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2519 1.34 - 1.46: 1643 1.46 - 1.58: 3900 1.58 - 1.70: 0 1.70 - 1.82: 85 Bond restraints: 8147 Sorted by residual: bond pdb=" OAF NKP R 401 " pdb=" PAC NKP R 401 " ideal model delta sigma weight residual 1.638 1.818 -0.180 2.00e-02 2.50e+03 8.10e+01 bond pdb=" OAD NKP R 401 " pdb=" PAC NKP R 401 " ideal model delta sigma weight residual 1.696 1.521 0.175 2.00e-02 2.50e+03 7.61e+01 bond pdb=" OAB NKP R 401 " pdb=" PAC NKP R 401 " ideal model delta sigma weight residual 1.683 1.512 0.171 2.00e-02 2.50e+03 7.34e+01 bond pdb=" CAG NKP R 401 " pdb=" OAF NKP R 401 " ideal model delta sigma weight residual 1.450 1.342 0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" CAH NKP R 401 " pdb=" OBC NKP R 401 " ideal model delta sigma weight residual 1.468 1.389 0.079 2.00e-02 2.50e+03 1.56e+01 ... (remaining 8142 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.41: 11068 12.41 - 24.81: 1 24.81 - 37.22: 0 37.22 - 49.62: 0 49.62 - 62.03: 1 Bond angle restraints: 11070 Sorted by residual: angle pdb=" OAB NKP R 401 " pdb=" PAC NKP R 401 " pdb=" OAD NKP R 401 " ideal model delta sigma weight residual 53.21 115.24 -62.03 3.00e+00 1.11e-01 4.28e+02 angle pdb=" N TRP R 82 " pdb=" CA TRP R 82 " pdb=" C TRP R 82 " ideal model delta sigma weight residual 109.79 120.10 -10.31 1.60e+00 3.91e-01 4.15e+01 angle pdb=" OAB NKP R 401 " pdb=" PAC NKP R 401 " pdb=" OAF NKP R 401 " ideal model delta sigma weight residual 115.22 100.97 14.25 3.00e+00 1.11e-01 2.26e+01 angle pdb=" N ALA A 351 " pdb=" CA ALA A 351 " pdb=" C ALA A 351 " ideal model delta sigma weight residual 111.07 116.08 -5.01 1.07e+00 8.73e-01 2.19e+01 angle pdb=" N ALA B 203 " pdb=" CA ALA B 203 " pdb=" C ALA B 203 " ideal model delta sigma weight residual 108.34 113.75 -5.41 1.31e+00 5.83e-01 1.71e+01 ... (remaining 11065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 4509 17.05 - 34.10: 390 34.10 - 51.16: 58 51.16 - 68.21: 12 68.21 - 85.26: 8 Dihedral angle restraints: 4977 sinusoidal: 2009 harmonic: 2968 Sorted by residual: dihedral pdb=" CB CYS R 89 " pdb=" SG CYS R 89 " pdb=" SG CYS R 168 " pdb=" CB CYS R 168 " ideal model delta sinusoidal sigma weight residual 93.00 165.13 -72.13 1 1.00e+01 1.00e-02 6.65e+01 dihedral pdb=" CA ASP B 291 " pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta harmonic sigma weight residual 180.00 153.17 26.83 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA VAL N 110 " pdb=" C VAL N 110 " pdb=" N THR N 111 " pdb=" CA THR N 111 " ideal model delta harmonic sigma weight residual -180.00 -160.23 -19.77 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 4974 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1108 0.070 - 0.139: 153 0.139 - 0.209: 15 0.209 - 0.279: 7 0.279 - 0.348: 5 Chirality restraints: 1288 Sorted by residual: chirality pdb=" CAH NKP R 401 " pdb=" CAG NKP R 401 " pdb=" CAI NKP R 401 " pdb=" OBC NKP R 401 " both_signs ideal model delta sigma weight residual False -2.84 -2.50 -0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" C14 CLR R 403 " pdb=" C13 CLR R 403 " pdb=" C15 CLR R 403 " pdb=" C8 CLR R 403 " both_signs ideal model delta sigma weight residual False -2.32 -2.65 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA TRP R 82 " pdb=" N TRP R 82 " pdb=" C TRP R 82 " pdb=" CB TRP R 82 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 1285 not shown) Planarity restraints: 1379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 82 " 0.019 2.00e-02 2.50e+03 1.27e-02 4.02e+00 pdb=" CG TRP B 82 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP B 82 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP B 82 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 82 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 82 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 82 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 82 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 82 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 82 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 41 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.74e+00 pdb=" C ILE R 41 " -0.033 2.00e-02 2.50e+03 pdb=" O ILE R 41 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE R 42 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 195 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.05e+00 pdb=" N PRO R 196 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO R 196 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO R 196 " -0.025 5.00e-02 4.00e+02 ... (remaining 1376 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 179 2.70 - 3.25: 7335 3.25 - 3.80: 11409 3.80 - 4.35: 14992 4.35 - 4.90: 26387 Nonbonded interactions: 60302 Sorted by model distance: nonbonded pdb=" O ASN R 50 " pdb=" OG1 THR R 53 " model vdw 2.154 3.040 nonbonded pdb=" O THR R 179 " pdb=" NH1 ARG R 183 " model vdw 2.274 3.120 nonbonded pdb=" OE2 GLU A 27 " pdb=" NZ LYS B 89 " model vdw 2.309 3.120 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.315 3.040 nonbonded pdb=" OH TYR A 391 " pdb=" NH2 ARG R 128 " model vdw 2.339 3.120 ... (remaining 60297 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.590 Find NCS groups from input model: 0.030 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: 0.010 Load rotamer database and sin/cos tables:7.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 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 0.180 8149 Z= 0.287 Angle : 1.039 62.029 11074 Z= 0.493 Chirality : 0.056 0.348 1288 Planarity : 0.004 0.044 1379 Dihedral : 13.254 85.261 3047 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.26), residues: 997 helix: 1.04 (0.27), residues: 371 sheet: 0.90 (0.36), residues: 207 loop : -1.37 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 98 TYR 0.016 0.002 TYR A 360 PHE 0.021 0.002 PHE B 292 TRP 0.034 0.003 TRP B 82 HIS 0.007 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00602 ( 8147) covalent geometry : angle 1.03909 (11070) SS BOND : bond 0.00150 ( 2) SS BOND : angle 1.01506 ( 4) hydrogen bonds : bond 0.13831 ( 377) hydrogen bonds : angle 5.47104 ( 1071) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 365 CYS cc_start: 0.6970 (p) cc_final: 0.6723 (p) REVERT: R 270 ARG cc_start: 0.7932 (ttm-80) cc_final: 0.7716 (mtt180) REVERT: G 36 ASP cc_start: 0.7472 (m-30) cc_final: 0.6971 (m-30) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.5098 time to fit residues: 67.8808 Evaluate side-chains 102 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.123735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.094313 restraints weight = 11876.814| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.93 r_work: 0.3069 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8149 Z= 0.141 Angle : 0.582 6.280 11074 Z= 0.313 Chirality : 0.044 0.151 1288 Planarity : 0.004 0.039 1379 Dihedral : 7.742 77.243 1329 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.30 % Allowed : 10.20 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.39 (0.27), residues: 997 helix: 1.35 (0.28), residues: 388 sheet: 0.97 (0.34), residues: 224 loop : -1.33 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 98 TYR 0.019 0.002 TYR B 105 PHE 0.016 0.002 PHE R 75 TRP 0.030 0.002 TRP B 82 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8147) covalent geometry : angle 0.58197 (11070) SS BOND : bond 0.00077 ( 2) SS BOND : angle 0.88183 ( 4) hydrogen bonds : bond 0.06024 ( 377) hydrogen bonds : angle 4.17186 ( 1071) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.307 Fit side-chains REVERT: A 60 MET cc_start: 0.6465 (OUTLIER) cc_final: 0.4651 (mtt) REVERT: A 302 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7997 (mp) REVERT: B 258 ASP cc_start: 0.8319 (t0) cc_final: 0.8061 (t0) REVERT: R 56 MET cc_start: 0.7759 (mtt) cc_final: 0.7378 (mtm) REVERT: G 36 ASP cc_start: 0.7891 (m-30) cc_final: 0.7347 (m-30) outliers start: 11 outliers final: 6 residues processed: 106 average time/residue: 0.4713 time to fit residues: 53.0505 Evaluate side-chains 102 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 248 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 37 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 24 optimal weight: 0.3980 chunk 50 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.125802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.096715 restraints weight = 11729.044| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.91 r_work: 0.3113 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8149 Z= 0.111 Angle : 0.516 5.790 11074 Z= 0.278 Chirality : 0.042 0.149 1288 Planarity : 0.003 0.034 1379 Dihedral : 7.074 72.715 1329 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.37 % Allowed : 10.44 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.27), residues: 997 helix: 1.56 (0.28), residues: 390 sheet: 1.13 (0.34), residues: 222 loop : -1.26 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 98 TYR 0.015 0.001 TYR B 105 PHE 0.013 0.001 PHE A 212 TRP 0.027 0.002 TRP B 82 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 8147) covalent geometry : angle 0.51609 (11070) SS BOND : bond 0.00169 ( 2) SS BOND : angle 0.76802 ( 4) hydrogen bonds : bond 0.04960 ( 377) hydrogen bonds : angle 3.87579 ( 1071) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.6185 (OUTLIER) cc_final: 0.4399 (mtt) REVERT: A 302 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7939 (mp) REVERT: B 234 PHE cc_start: 0.9107 (OUTLIER) cc_final: 0.7739 (m-80) REVERT: B 258 ASP cc_start: 0.8224 (t0) cc_final: 0.7927 (t0) REVERT: N 37 VAL cc_start: 0.8222 (t) cc_final: 0.7737 (m) REVERT: N 86 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8082 (mm) REVERT: R 23 MET cc_start: 0.7506 (mmm) cc_final: 0.6985 (mmp) REVERT: R 45 VAL cc_start: 0.7951 (t) cc_final: 0.7551 (p) REVERT: G 47 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8088 (mt-10) outliers start: 20 outliers final: 8 residues processed: 113 average time/residue: 0.4720 time to fit residues: 57.0561 Evaluate side-chains 116 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 44 CYS Chi-restraints excluded: chain R residue 68 PHE Chi-restraints excluded: chain R residue 248 ASN Chi-restraints excluded: chain G residue 47 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 67 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 73 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN R 200 ASN R 248 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.122443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.092819 restraints weight = 11860.789| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.01 r_work: 0.3047 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8149 Z= 0.179 Angle : 0.621 8.280 11074 Z= 0.330 Chirality : 0.045 0.172 1288 Planarity : 0.004 0.040 1379 Dihedral : 7.247 72.603 1329 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.32 % Allowed : 10.91 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.52 (0.27), residues: 997 helix: 1.49 (0.28), residues: 390 sheet: 0.96 (0.35), residues: 214 loop : -1.21 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 72 TYR 0.020 0.002 TYR B 105 PHE 0.015 0.002 PHE A 212 TRP 0.024 0.002 TRP B 82 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 8147) covalent geometry : angle 0.62118 (11070) SS BOND : bond 0.00051 ( 2) SS BOND : angle 1.09194 ( 4) hydrogen bonds : bond 0.06455 ( 377) hydrogen bonds : angle 4.07608 ( 1071) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.317 Fit side-chains REVERT: A 60 MET cc_start: 0.6405 (OUTLIER) cc_final: 0.4479 (mtt) REVERT: A 294 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7908 (mm110) REVERT: A 302 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7996 (mp) REVERT: A 314 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.6588 (mp0) REVERT: B 44 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8226 (mp-120) REVERT: B 59 TYR cc_start: 0.8939 (OUTLIER) cc_final: 0.8566 (m-80) REVERT: B 234 PHE cc_start: 0.9147 (OUTLIER) cc_final: 0.7719 (m-80) REVERT: B 258 ASP cc_start: 0.8261 (t0) cc_final: 0.7990 (t0) REVERT: N 86 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8136 (mm) REVERT: R 23 MET cc_start: 0.7470 (mmm) cc_final: 0.6941 (mmp) REVERT: R 45 VAL cc_start: 0.7913 (t) cc_final: 0.7533 (p) REVERT: G 36 ASP cc_start: 0.7883 (m-30) cc_final: 0.7337 (m-30) REVERT: G 47 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8077 (mt-10) outliers start: 28 outliers final: 15 residues processed: 119 average time/residue: 0.5358 time to fit residues: 67.8485 Evaluate side-chains 119 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 44 CYS Chi-restraints excluded: chain R residue 68 PHE Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain G residue 47 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 27 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN R 200 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.124485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.095887 restraints weight = 11767.236| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.91 r_work: 0.3076 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8149 Z= 0.135 Angle : 0.563 6.636 11074 Z= 0.302 Chirality : 0.043 0.176 1288 Planarity : 0.004 0.036 1379 Dihedral : 7.090 72.573 1329 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.49 % Allowed : 13.40 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.63 (0.27), residues: 997 helix: 1.58 (0.28), residues: 390 sheet: 1.04 (0.34), residues: 224 loop : -1.22 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 98 TYR 0.014 0.001 TYR B 105 PHE 0.014 0.001 PHE A 212 TRP 0.028 0.002 TRP B 82 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8147) covalent geometry : angle 0.56250 (11070) SS BOND : bond 0.00079 ( 2) SS BOND : angle 0.85058 ( 4) hydrogen bonds : bond 0.05635 ( 377) hydrogen bonds : angle 3.96861 ( 1071) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.6397 (OUTLIER) cc_final: 0.4577 (mtt) REVERT: A 302 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8002 (mp) REVERT: B 59 TYR cc_start: 0.8879 (OUTLIER) cc_final: 0.8437 (m-80) REVERT: B 234 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.7860 (m-80) REVERT: B 258 ASP cc_start: 0.8265 (t0) cc_final: 0.7993 (t0) REVERT: N 37 VAL cc_start: 0.8288 (t) cc_final: 0.7844 (m) REVERT: R 23 MET cc_start: 0.7500 (mmm) cc_final: 0.7014 (mmp) REVERT: R 45 VAL cc_start: 0.7843 (t) cc_final: 0.7485 (p) REVERT: G 47 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8096 (mt-10) outliers start: 21 outliers final: 13 residues processed: 109 average time/residue: 0.4596 time to fit residues: 53.6269 Evaluate side-chains 113 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 44 CYS Chi-restraints excluded: chain R residue 68 PHE Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 248 ASN Chi-restraints excluded: chain G residue 47 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 44 optimal weight: 0.2980 chunk 94 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 74 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 44 GLN R 81 ASN R 200 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.126110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.096835 restraints weight = 11772.750| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.93 r_work: 0.3112 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8149 Z= 0.114 Angle : 0.522 7.345 11074 Z= 0.280 Chirality : 0.042 0.186 1288 Planarity : 0.003 0.034 1379 Dihedral : 6.772 71.393 1329 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.73 % Allowed : 13.29 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.27), residues: 997 helix: 1.74 (0.28), residues: 390 sheet: 1.06 (0.34), residues: 224 loop : -1.11 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 98 TYR 0.010 0.001 TYR B 59 PHE 0.013 0.001 PHE A 212 TRP 0.027 0.002 TRP B 82 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 8147) covalent geometry : angle 0.52203 (11070) SS BOND : bond 0.00107 ( 2) SS BOND : angle 0.72616 ( 4) hydrogen bonds : bond 0.04876 ( 377) hydrogen bonds : angle 3.82338 ( 1071) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.6176 (OUTLIER) cc_final: 0.4356 (mtt) REVERT: A 302 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7975 (mp) REVERT: B 45 MET cc_start: 0.8820 (mtt) cc_final: 0.8485 (mtt) REVERT: B 59 TYR cc_start: 0.8833 (OUTLIER) cc_final: 0.8289 (m-80) REVERT: B 234 PHE cc_start: 0.9076 (OUTLIER) cc_final: 0.7865 (m-80) REVERT: N 37 VAL cc_start: 0.8215 (t) cc_final: 0.7846 (m) REVERT: R 23 MET cc_start: 0.7484 (mmm) cc_final: 0.6965 (mmp) REVERT: R 45 VAL cc_start: 0.7683 (t) cc_final: 0.7323 (p) REVERT: G 47 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8074 (mt-10) outliers start: 23 outliers final: 13 residues processed: 119 average time/residue: 0.4670 time to fit residues: 59.4668 Evaluate side-chains 116 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 44 CYS Chi-restraints excluded: chain R residue 68 PHE Chi-restraints excluded: chain R residue 248 ASN Chi-restraints excluded: chain R residue 263 CYS Chi-restraints excluded: chain G residue 47 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 4 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.123288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.094829 restraints weight = 11807.006| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.88 r_work: 0.3058 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8149 Z= 0.167 Angle : 0.609 8.122 11074 Z= 0.323 Chirality : 0.045 0.193 1288 Planarity : 0.004 0.037 1379 Dihedral : 6.902 70.293 1329 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.97 % Allowed : 13.76 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.65 (0.27), residues: 997 helix: 1.66 (0.28), residues: 386 sheet: 1.00 (0.34), residues: 224 loop : -1.22 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 72 TYR 0.014 0.002 TYR B 105 PHE 0.016 0.002 PHE B 234 TRP 0.023 0.002 TRP B 82 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 8147) covalent geometry : angle 0.60894 (11070) SS BOND : bond 0.00044 ( 2) SS BOND : angle 0.97993 ( 4) hydrogen bonds : bond 0.06155 ( 377) hydrogen bonds : angle 4.02942 ( 1071) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.6509 (OUTLIER) cc_final: 0.4604 (mtt) REVERT: A 294 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7910 (mm110) REVERT: A 302 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8021 (mp) REVERT: B 59 TYR cc_start: 0.8942 (OUTLIER) cc_final: 0.8530 (m-80) REVERT: B 234 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.7771 (m-80) REVERT: N 37 VAL cc_start: 0.8322 (t) cc_final: 0.7890 (m) REVERT: R 23 MET cc_start: 0.7499 (mmm) cc_final: 0.7033 (mmp) REVERT: R 45 VAL cc_start: 0.7783 (t) cc_final: 0.7430 (p) REVERT: G 47 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8092 (mt-10) outliers start: 25 outliers final: 18 residues processed: 114 average time/residue: 0.4552 time to fit residues: 55.5851 Evaluate side-chains 120 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 44 CYS Chi-restraints excluded: chain R residue 68 PHE Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 248 ASN Chi-restraints excluded: chain R residue 263 CYS Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 47 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 58 optimal weight: 0.8980 chunk 27 optimal weight: 0.0470 chunk 17 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 77 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 56 optimal weight: 0.2980 chunk 73 optimal weight: 0.7980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN R 81 ASN R 200 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.126603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.098338 restraints weight = 11779.476| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.89 r_work: 0.3118 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8149 Z= 0.105 Angle : 0.511 8.489 11074 Z= 0.275 Chirality : 0.042 0.172 1288 Planarity : 0.003 0.034 1379 Dihedral : 6.401 69.174 1329 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.37 % Allowed : 14.47 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.27), residues: 997 helix: 1.86 (0.28), residues: 385 sheet: 1.07 (0.35), residues: 214 loop : -1.08 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 98 TYR 0.011 0.001 TYR B 59 PHE 0.012 0.001 PHE A 212 TRP 0.028 0.002 TRP B 82 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 8147) covalent geometry : angle 0.51100 (11070) SS BOND : bond 0.00095 ( 2) SS BOND : angle 0.68128 ( 4) hydrogen bonds : bond 0.04623 ( 377) hydrogen bonds : angle 3.78440 ( 1071) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.6173 (OUTLIER) cc_final: 0.4416 (mtt) REVERT: A 302 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7925 (mp) REVERT: B 59 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.8167 (m-80) REVERT: B 234 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.7812 (m-80) REVERT: N 37 VAL cc_start: 0.8204 (t) cc_final: 0.7833 (m) REVERT: R 23 MET cc_start: 0.7493 (mmm) cc_final: 0.7008 (mmp) REVERT: G 47 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8078 (mt-10) outliers start: 20 outliers final: 15 residues processed: 113 average time/residue: 0.4560 time to fit residues: 55.3163 Evaluate side-chains 118 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain R residue 68 PHE Chi-restraints excluded: chain R residue 248 ASN Chi-restraints excluded: chain R residue 263 CYS Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 52 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 66 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 38 optimal weight: 0.0980 chunk 58 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN R 81 ASN R 200 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.126029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.097671 restraints weight = 11731.961| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.91 r_work: 0.3108 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8149 Z= 0.114 Angle : 0.524 9.277 11074 Z= 0.281 Chirality : 0.042 0.201 1288 Planarity : 0.003 0.034 1379 Dihedral : 6.193 67.632 1329 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.61 % Allowed : 14.23 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.27), residues: 997 helix: 1.88 (0.28), residues: 385 sheet: 1.09 (0.35), residues: 214 loop : -1.02 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 98 TYR 0.014 0.001 TYR R 40 PHE 0.013 0.001 PHE A 212 TRP 0.024 0.002 TRP B 82 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 8147) covalent geometry : angle 0.52424 (11070) SS BOND : bond 0.00099 ( 2) SS BOND : angle 0.69260 ( 4) hydrogen bonds : bond 0.04824 ( 377) hydrogen bonds : angle 3.79281 ( 1071) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.6302 (OUTLIER) cc_final: 0.4469 (mtt) REVERT: A 302 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7955 (mp) REVERT: B 59 TYR cc_start: 0.8840 (OUTLIER) cc_final: 0.8299 (m-80) REVERT: B 234 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.7770 (m-80) REVERT: N 37 VAL cc_start: 0.8216 (t) cc_final: 0.7862 (m) REVERT: R 23 MET cc_start: 0.7601 (mmm) cc_final: 0.7154 (mmp) REVERT: G 47 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8050 (mt-10) outliers start: 22 outliers final: 15 residues processed: 114 average time/residue: 0.4622 time to fit residues: 56.3348 Evaluate side-chains 120 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain R residue 68 PHE Chi-restraints excluded: chain R residue 248 ASN Chi-restraints excluded: chain R residue 263 CYS Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 73 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 85 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN R 81 ASN R 200 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.125197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.096884 restraints weight = 11836.593| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.90 r_work: 0.3098 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8149 Z= 0.128 Angle : 0.550 9.775 11074 Z= 0.294 Chirality : 0.043 0.182 1288 Planarity : 0.004 0.034 1379 Dihedral : 6.145 67.055 1329 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.61 % Allowed : 14.23 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.87 (0.27), residues: 997 helix: 1.85 (0.28), residues: 385 sheet: 1.07 (0.34), residues: 224 loop : -1.07 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 98 TYR 0.010 0.001 TYR A 360 PHE 0.014 0.001 PHE A 212 TRP 0.025 0.002 TRP B 82 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8147) covalent geometry : angle 0.54967 (11070) SS BOND : bond 0.00074 ( 2) SS BOND : angle 0.76732 ( 4) hydrogen bonds : bond 0.05134 ( 377) hydrogen bonds : angle 3.85196 ( 1071) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.6317 (OUTLIER) cc_final: 0.4462 (mtt) REVERT: A 302 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7988 (mp) REVERT: B 59 TYR cc_start: 0.8860 (OUTLIER) cc_final: 0.8324 (m-80) REVERT: B 234 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.7800 (m-80) REVERT: N 37 VAL cc_start: 0.8228 (t) cc_final: 0.7873 (m) REVERT: R 23 MET cc_start: 0.7587 (mmm) cc_final: 0.7143 (mmp) REVERT: G 47 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8062 (mt-10) outliers start: 22 outliers final: 17 residues processed: 115 average time/residue: 0.4943 time to fit residues: 60.9909 Evaluate side-chains 122 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain R residue 44 CYS Chi-restraints excluded: chain R residue 68 PHE Chi-restraints excluded: chain R residue 248 ASN Chi-restraints excluded: chain R residue 263 CYS Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 67 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN N 31 ASN R 81 ASN R 200 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.124541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.096173 restraints weight = 11654.276| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.90 r_work: 0.3082 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8149 Z= 0.146 Angle : 0.571 8.187 11074 Z= 0.305 Chirality : 0.043 0.182 1288 Planarity : 0.004 0.034 1379 Dihedral : 6.185 66.822 1329 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.73 % Allowed : 14.23 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.82 (0.27), residues: 997 helix: 1.80 (0.28), residues: 385 sheet: 1.05 (0.34), residues: 224 loop : -1.08 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 98 TYR 0.011 0.001 TYR A 360 PHE 0.014 0.002 PHE A 212 TRP 0.024 0.002 TRP B 82 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 8147) covalent geometry : angle 0.57068 (11070) SS BOND : bond 0.00054 ( 2) SS BOND : angle 0.83321 ( 4) hydrogen bonds : bond 0.05453 ( 377) hydrogen bonds : angle 3.89764 ( 1071) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2680.44 seconds wall clock time: 46 minutes 22.48 seconds (2782.48 seconds total)