Starting phenix.real_space_refine on Tue Mar 3 21:34:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f4f_31449/03_2026/7f4f_31449.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f4f_31449/03_2026/7f4f_31449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f4f_31449/03_2026/7f4f_31449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f4f_31449/03_2026/7f4f_31449.map" model { file = "/net/cci-nas-00/data/ceres_data/7f4f_31449/03_2026/7f4f_31449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f4f_31449/03_2026/7f4f_31449.cif" } resolution = 2.9 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= 0.004 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 Ca 1 9.91 5 S 59 5.16 5 C 5647 2.51 5 N 1537 2.21 5 O 1637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8881 Number of models: 1 Model: "" Number of chains: 8 Chain: "S" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Chain: "R" Number of atoms: 2079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2079 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 6, 'TRANS': 262} Chain breaks: 1 Chain: "A" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1916 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 423 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2583 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 32 Chain: "F" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 45 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'NLE:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 63 Classifications: {'peptide': 7} Modifications used: {'PEPT-D': 1} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.14, per 1000 atoms: 0.24 Number of scatterers: 8881 At special positions: 0 Unit cell: (113.905, 99.275, 115.995, 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) Ca 1 19.99 S 59 16.00 O 1637 8.00 N 1537 7.00 C 5647 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Simple disulfide: pdb=" SG CYS R 267 " - pdb=" SG CYS R 273 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " DPN F 7 " - " HIS F 6 " Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 339.9 milliseconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DPN F 7 " Number of C-beta restraints generated: 2134 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 12 sheets defined 40.6% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.084A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'S' and resid 220 through 224 Processing helix chain 'R' and resid 41 through 66 Processing helix chain 'R' and resid 71 through 103 Processing helix chain 'R' and resid 109 through 148 Processing helix chain 'R' and resid 151 through 156 Processing helix chain 'R' and resid 157 through 182 Processing helix chain 'R' and resid 185 through 226 removed outlier: 3.787A pdb=" N LEU R 189 " --> pdb=" O HIS R 185 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 267 Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 270 through 278 Processing helix chain 'R' and resid 279 through 299 Proline residue: R 295 - end of helix Processing helix chain 'R' and resid 302 through 314 Processing helix chain 'A' and resid 13 through 40 Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 252 through 279 removed outlier: 4.524A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.902A pdb=" N PHE A 312 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 4.164A pdb=" N ARG A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.624A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'G' and resid 10 through 25 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing sheet with id=AA1, first strand: chain 'S' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.245A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AA4, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.736A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.214A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA7, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.527A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.850A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.680A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.571A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.488A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.723A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) 488 hydrogen bonds defined for protein. 1380 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: 1.71 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 1442 1.31 - 1.44: 2474 1.44 - 1.57: 5054 1.57 - 1.71: 6 1.71 - 1.84: 83 Bond restraints: 9059 Sorted by residual: bond pdb=" C ALA A 269 " pdb=" O ALA A 269 " ideal model delta sigma weight residual 1.237 1.201 0.036 1.17e-02 7.31e+03 9.40e+00 bond pdb=" C NLE F 4 " pdb=" O NLE F 4 " ideal model delta sigma weight residual 1.231 1.172 0.059 2.00e-02 2.50e+03 8.78e+00 bond pdb=" CA ILE A 288 " pdb=" CB ILE A 288 " ideal model delta sigma weight residual 1.527 1.490 0.036 1.31e-02 5.83e+03 7.76e+00 bond pdb=" CA ALA A 269 " pdb=" CB ALA A 269 " ideal model delta sigma weight residual 1.528 1.570 -0.042 1.56e-02 4.11e+03 7.14e+00 bond pdb=" CD GLN R 219 " pdb=" OE1 GLN R 219 " ideal model delta sigma weight residual 1.231 1.181 0.050 1.90e-02 2.77e+03 7.00e+00 ... (remaining 9054 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 11620 2.16 - 4.32: 591 4.32 - 6.48: 50 6.48 - 8.64: 8 8.64 - 10.80: 6 Bond angle restraints: 12275 Sorted by residual: angle pdb=" N GLY B 216 " pdb=" CA GLY B 216 " pdb=" C GLY B 216 " ideal model delta sigma weight residual 115.43 120.64 -5.21 1.41e+00 5.03e-01 1.37e+01 angle pdb=" C TYR S 190 " pdb=" N ARG S 191 " pdb=" CA ARG S 191 " ideal model delta sigma weight residual 121.32 113.58 7.74 2.10e+00 2.27e-01 1.36e+01 angle pdb=" N LEU R 206 " pdb=" CA LEU R 206 " pdb=" C LEU R 206 " ideal model delta sigma weight residual 110.97 114.92 -3.95 1.09e+00 8.42e-01 1.31e+01 angle pdb=" CA TYR S 190 " pdb=" CB TYR S 190 " pdb=" CG TYR S 190 " ideal model delta sigma weight residual 113.90 120.25 -6.35 1.80e+00 3.09e-01 1.24e+01 angle pdb=" C ARG R 109 " pdb=" N ALA R 110 " pdb=" CA ALA R 110 " ideal model delta sigma weight residual 120.28 124.62 -4.34 1.34e+00 5.57e-01 1.05e+01 ... (remaining 12270 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 4966 17.02 - 34.05: 352 34.05 - 51.07: 44 51.07 - 68.09: 13 68.09 - 85.12: 8 Dihedral angle restraints: 5383 sinusoidal: 2079 harmonic: 3304 Sorted by residual: dihedral pdb=" CA PRO S 236 " pdb=" C PRO S 236 " pdb=" N LEU S 237 " pdb=" CA LEU S 237 " ideal model delta harmonic sigma weight residual 180.00 148.78 31.22 0 5.00e+00 4.00e-02 3.90e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 150.75 29.25 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA TRP B 339 " pdb=" C TRP B 339 " pdb=" N ASN B 340 " pdb=" CA ASN B 340 " ideal model delta harmonic sigma weight residual 180.00 150.84 29.16 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 5380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 968 0.062 - 0.124: 367 0.124 - 0.186: 58 0.186 - 0.248: 7 0.248 - 0.310: 7 Chirality restraints: 1407 Sorted by residual: chirality pdb=" CG LEU A 270 " pdb=" CB LEU A 270 " pdb=" CD1 LEU A 270 " pdb=" CD2 LEU A 270 " both_signs ideal model delta sigma weight residual False -2.59 -2.90 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CG LEU A 291 " pdb=" CB LEU A 291 " pdb=" CD1 LEU A 291 " pdb=" CD2 LEU A 291 " both_signs ideal model delta sigma weight residual False -2.59 -2.89 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CG LEU S 174 " pdb=" CB LEU S 174 " pdb=" CD1 LEU S 174 " pdb=" CD2 LEU S 174 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 1404 not shown) Planarity restraints: 1555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 340 " -0.042 2.00e-02 2.50e+03 8.45e-02 7.14e+01 pdb=" C ASN B 340 " 0.146 2.00e-02 2.50e+03 pdb=" O ASN B 340 " -0.056 2.00e-02 2.50e+03 pdb=" N GLY B 341 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG S 191 " -0.373 9.50e-02 1.11e+02 1.71e-01 3.34e+01 pdb=" NE ARG S 191 " 0.046 2.00e-02 2.50e+03 pdb=" CZ ARG S 191 " -0.065 2.00e-02 2.50e+03 pdb=" NH1 ARG S 191 " 0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG S 191 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG S 67 " 0.254 9.50e-02 1.11e+02 1.16e-01 1.37e+01 pdb=" NE ARG S 67 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG S 67 " 0.039 2.00e-02 2.50e+03 pdb=" NH1 ARG S 67 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG S 67 " -0.005 2.00e-02 2.50e+03 ... (remaining 1552 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 351 2.71 - 3.26: 9284 3.26 - 3.81: 15108 3.81 - 4.35: 19926 4.35 - 4.90: 33099 Nonbonded interactions: 77768 Sorted by model distance: nonbonded pdb=" OH TYR S 175 " pdb=" OE2 GLU A 15 " model vdw 2.164 3.040 nonbonded pdb=" O LEU R 259 " pdb=" OG1 THR R 262 " model vdw 2.227 3.040 nonbonded pdb=" OD1 ASP A 295 " pdb=" N LEU A 296 " model vdw 2.233 3.120 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.242 3.040 nonbonded pdb=" OD1 ASN R 118 " pdb=" NH2 ARG F 8 " model vdw 2.270 3.120 ... (remaining 77763 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: 0.740 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.360 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:8.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 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 : 0.010 0.069 9062 Z= 0.510 Angle : 1.093 10.799 12282 Z= 0.635 Chirality : 0.064 0.310 1407 Planarity : 0.012 0.171 1554 Dihedral : 12.597 85.116 3240 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.89 (0.24), residues: 1115 helix: -0.45 (0.22), residues: 411 sheet: -0.46 (0.30), residues: 296 loop : -0.57 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.070 0.006 ARG S 191 TYR 0.039 0.007 TYR B 105 PHE 0.025 0.005 PHE R 300 TRP 0.043 0.007 TRP B 339 HIS 0.020 0.004 HIS A 387 Details of bonding type rmsd covalent geometry : bond 0.00962 ( 9059) covalent geometry : angle 1.09281 (12275) SS BOND : bond 0.00955 ( 2) SS BOND : angle 0.92565 ( 4) hydrogen bonds : bond 0.13106 ( 488) hydrogen bonds : angle 6.79327 ( 1380) link_TRANS : bond 0.00784 ( 1) link_TRANS : angle 0.68370 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 GLN cc_start: 0.7960 (mt0) cc_final: 0.7738 (mt0) REVERT: A 271 ASN cc_start: 0.7834 (m110) cc_final: 0.7587 (m110) REVERT: A 339 TYR cc_start: 0.7520 (m-80) cc_final: 0.6907 (m-80) REVERT: B 264 TYR cc_start: 0.8710 (m-80) cc_final: 0.8493 (m-80) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.6678 time to fit residues: 159.9842 Evaluate side-chains 149 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 142 GLN S 179 GLN S 183 GLN R 68 ASN R 91 ASN R 270 HIS ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A 294 GLN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN B 91 HIS B 176 GLN B 230 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.093580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.071479 restraints weight = 16902.520| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.78 r_work: 0.2909 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9062 Z= 0.158 Angle : 0.655 9.121 12282 Z= 0.346 Chirality : 0.044 0.213 1407 Planarity : 0.005 0.051 1554 Dihedral : 5.855 41.506 1242 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.30 % Allowed : 10.86 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.26), residues: 1115 helix: 1.66 (0.25), residues: 410 sheet: -0.49 (0.31), residues: 269 loop : 0.14 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 342 TYR 0.014 0.001 TYR S 235 PHE 0.017 0.002 PHE R 147 TRP 0.025 0.002 TRP B 339 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9059) covalent geometry : angle 0.65510 (12275) SS BOND : bond 0.00281 ( 2) SS BOND : angle 0.73919 ( 4) hydrogen bonds : bond 0.04807 ( 488) hydrogen bonds : angle 5.39513 ( 1380) link_TRANS : bond 0.00115 ( 1) link_TRANS : angle 0.17473 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: S 73 ASP cc_start: 0.7586 (t0) cc_final: 0.7345 (t0) REVERT: S 85 SER cc_start: 0.9218 (t) cc_final: 0.9001 (p) REVERT: S 89 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7716 (tm-30) REVERT: S 93 MET cc_start: 0.8834 (ttm) cc_final: 0.8591 (tpp) REVERT: S 153 GLU cc_start: 0.7598 (tt0) cc_final: 0.7305 (tt0) REVERT: S 183 GLN cc_start: 0.8309 (mt0) cc_final: 0.7954 (mt0) REVERT: S 222 GLU cc_start: 0.8582 (pt0) cc_final: 0.8169 (pp20) REVERT: S 223 ASP cc_start: 0.8803 (m-30) cc_final: 0.8093 (m-30) REVERT: S 234 GLU cc_start: 0.8988 (pt0) cc_final: 0.8675 (pt0) REVERT: R 42 ASP cc_start: 0.8947 (m-30) cc_final: 0.8726 (m-30) REVERT: R 191 CYS cc_start: 0.8780 (m) cc_final: 0.8292 (m) REVERT: R 215 CYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7961 (t) REVERT: R 294 ASP cc_start: 0.8143 (m-30) cc_final: 0.7654 (m-30) REVERT: A 236 GLN cc_start: 0.8887 (mt0) cc_final: 0.8672 (mt0) REVERT: A 390 GLN cc_start: 0.8701 (tt0) cc_final: 0.8304 (tt0) REVERT: G 20 LYS cc_start: 0.8646 (ttpp) cc_final: 0.7864 (ptpp) REVERT: B 10 GLU cc_start: 0.8858 (tp30) cc_final: 0.8441 (tp30) REVERT: B 32 GLN cc_start: 0.9011 (mt0) cc_final: 0.8809 (mt0) REVERT: B 145 TYR cc_start: 0.9302 (p90) cc_final: 0.9086 (p90) REVERT: B 172 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7913 (mm-30) REVERT: B 217 MET cc_start: 0.8161 (pmm) cc_final: 0.7903 (pmm) REVERT: B 254 ASP cc_start: 0.7904 (t70) cc_final: 0.7504 (t0) REVERT: B 262 MET cc_start: 0.8460 (tpp) cc_final: 0.8188 (ttm) REVERT: B 266 HIS cc_start: 0.8512 (OUTLIER) cc_final: 0.8075 (t70) outliers start: 22 outliers final: 4 residues processed: 174 average time/residue: 0.6194 time to fit residues: 114.0359 Evaluate side-chains 152 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 145 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 215 CYS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 275 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 43 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 91 ASN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN A 294 GLN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 237 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.091407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.069470 restraints weight = 16967.038| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.76 r_work: 0.2843 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9062 Z= 0.181 Angle : 0.613 8.287 12282 Z= 0.322 Chirality : 0.044 0.200 1407 Planarity : 0.005 0.051 1554 Dihedral : 5.301 39.078 1242 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.82 % Allowed : 12.53 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.26), residues: 1115 helix: 2.07 (0.24), residues: 410 sheet: -0.54 (0.31), residues: 276 loop : 0.36 (0.33), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 218 TYR 0.021 0.002 TYR S 190 PHE 0.020 0.002 PHE R 147 TRP 0.018 0.002 TRP B 339 HIS 0.005 0.001 HIS R 301 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 9059) covalent geometry : angle 0.61265 (12275) SS BOND : bond 0.00169 ( 2) SS BOND : angle 0.42276 ( 4) hydrogen bonds : bond 0.04328 ( 488) hydrogen bonds : angle 5.07930 ( 1380) link_TRANS : bond 0.00176 ( 1) link_TRANS : angle 0.22025 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: S 73 ASP cc_start: 0.7694 (t0) cc_final: 0.7243 (t0) REVERT: S 85 SER cc_start: 0.9165 (t) cc_final: 0.8936 (p) REVERT: S 89 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7817 (tm-30) REVERT: S 153 GLU cc_start: 0.7835 (tt0) cc_final: 0.7634 (tt0) REVERT: S 183 GLN cc_start: 0.8239 (mt0) cc_final: 0.7897 (mt0) REVERT: S 220 GLU cc_start: 0.8178 (pm20) cc_final: 0.7909 (pm20) REVERT: S 222 GLU cc_start: 0.8561 (pt0) cc_final: 0.8341 (pt0) REVERT: S 234 GLU cc_start: 0.8936 (pt0) cc_final: 0.8634 (pt0) REVERT: R 191 CYS cc_start: 0.8806 (m) cc_final: 0.8298 (m) REVERT: R 270 HIS cc_start: 0.8360 (OUTLIER) cc_final: 0.8131 (t-90) REVERT: R 303 GLN cc_start: 0.8687 (tp40) cc_final: 0.8372 (tm-30) REVERT: A 21 GLU cc_start: 0.8290 (tt0) cc_final: 0.7994 (tt0) REVERT: A 236 GLN cc_start: 0.9011 (mt0) cc_final: 0.8767 (mt0) REVERT: G 20 LYS cc_start: 0.8244 (ttpp) cc_final: 0.8005 (ptpp) REVERT: B 10 GLU cc_start: 0.9009 (tp30) cc_final: 0.8044 (tm-30) REVERT: B 32 GLN cc_start: 0.9106 (mt0) cc_final: 0.8807 (mt0) REVERT: B 172 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7971 (mm-30) REVERT: B 217 MET cc_start: 0.8548 (pmm) cc_final: 0.8232 (ppp) REVERT: B 254 ASP cc_start: 0.7971 (t70) cc_final: 0.7607 (t70) REVERT: B 262 MET cc_start: 0.8534 (tpp) cc_final: 0.8313 (ttm) REVERT: B 266 HIS cc_start: 0.8560 (OUTLIER) cc_final: 0.8033 (t70) REVERT: B 325 MET cc_start: 0.8994 (tpp) cc_final: 0.8759 (mmm) REVERT: F 11 LYS cc_start: 0.9388 (mttt) cc_final: 0.9070 (mmmm) outliers start: 27 outliers final: 5 residues processed: 171 average time/residue: 0.6887 time to fit residues: 124.1725 Evaluate side-chains 153 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain R residue 109 ARG Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 270 HIS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 266 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 30 optimal weight: 10.0000 chunk 2 optimal weight: 0.0870 chunk 107 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 97 optimal weight: 0.0980 chunk 42 optimal weight: 3.9990 overall best weight: 2.6364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 39 GLN S 179 GLN R 290 ASN A 59 GLN A 267 GLN A 371 ASN B 75 GLN B 175 GLN B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.087795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.064270 restraints weight = 17364.176| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.86 r_work: 0.2752 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 9062 Z= 0.258 Angle : 0.652 8.583 12282 Z= 0.341 Chirality : 0.045 0.198 1407 Planarity : 0.005 0.050 1554 Dihedral : 5.254 34.090 1242 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.03 % Allowed : 14.30 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.26), residues: 1115 helix: 2.20 (0.24), residues: 410 sheet: -0.57 (0.31), residues: 281 loop : 0.53 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 265 TYR 0.024 0.002 TYR S 190 PHE 0.021 0.002 PHE R 147 TRP 0.012 0.002 TRP B 339 HIS 0.006 0.001 HIS R 209 Details of bonding type rmsd covalent geometry : bond 0.00583 ( 9059) covalent geometry : angle 0.65257 (12275) SS BOND : bond 0.00181 ( 2) SS BOND : angle 0.39467 ( 4) hydrogen bonds : bond 0.04262 ( 488) hydrogen bonds : angle 5.10275 ( 1380) link_TRANS : bond 0.00421 ( 1) link_TRANS : angle 0.37237 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 73 ASP cc_start: 0.7723 (t0) cc_final: 0.7152 (t0) REVERT: S 85 SER cc_start: 0.9160 (t) cc_final: 0.8903 (p) REVERT: S 89 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7845 (tm-30) REVERT: S 183 GLN cc_start: 0.8401 (mt0) cc_final: 0.8032 (mt0) REVERT: S 220 GLU cc_start: 0.8321 (pm20) cc_final: 0.7462 (pm20) REVERT: S 222 GLU cc_start: 0.8634 (pt0) cc_final: 0.8295 (pm20) REVERT: S 223 ASP cc_start: 0.8900 (m-30) cc_final: 0.8074 (m-30) REVERT: R 42 ASP cc_start: 0.9063 (m-30) cc_final: 0.8857 (m-30) REVERT: R 65 LYS cc_start: 0.8301 (ttmt) cc_final: 0.7974 (mptt) REVERT: R 114 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8518 (tt0) REVERT: R 191 CYS cc_start: 0.8767 (m) cc_final: 0.8255 (m) REVERT: R 270 HIS cc_start: 0.8501 (OUTLIER) cc_final: 0.8201 (t-90) REVERT: R 290 ASN cc_start: 0.8499 (t0) cc_final: 0.8189 (t0) REVERT: R 311 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8485 (mp0) REVERT: A 21 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8258 (tt0) REVERT: A 236 GLN cc_start: 0.9043 (mt0) cc_final: 0.8763 (mt0) REVERT: A 369 THR cc_start: 0.9179 (p) cc_final: 0.8945 (m) REVERT: G 20 LYS cc_start: 0.8297 (ttpp) cc_final: 0.8083 (ptpp) REVERT: B 10 GLU cc_start: 0.9025 (tp30) cc_final: 0.8185 (tp30) REVERT: B 13 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8570 (pp30) REVERT: B 42 ARG cc_start: 0.7681 (tpt170) cc_final: 0.7411 (tpt170) REVERT: B 57 LYS cc_start: 0.8761 (mtmm) cc_final: 0.8529 (mtmm) REVERT: B 172 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8056 (mm-30) REVERT: B 217 MET cc_start: 0.8833 (pmm) cc_final: 0.8487 (ppp) REVERT: B 254 ASP cc_start: 0.8029 (t70) cc_final: 0.7656 (t70) REVERT: B 266 HIS cc_start: 0.8544 (OUTLIER) cc_final: 0.8130 (t70) REVERT: B 325 MET cc_start: 0.9019 (tpp) cc_final: 0.8774 (mmm) REVERT: F 11 LYS cc_start: 0.9406 (mttt) cc_final: 0.9084 (mmmm) outliers start: 29 outliers final: 9 residues processed: 164 average time/residue: 0.7017 time to fit residues: 121.1758 Evaluate side-chains 150 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 157 ILE Chi-restraints excluded: chain R residue 109 ARG Chi-restraints excluded: chain R residue 114 GLN Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 270 HIS Chi-restraints excluded: chain R residue 311 GLU Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 99 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 68 optimal weight: 0.0670 chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 39 GLN A 59 GLN A 267 GLN A 278 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.089968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.066956 restraints weight = 17084.054| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.84 r_work: 0.2806 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9062 Z= 0.150 Angle : 0.594 7.099 12282 Z= 0.309 Chirality : 0.042 0.202 1407 Planarity : 0.004 0.051 1554 Dihedral : 5.000 28.714 1242 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.51 % Allowed : 15.55 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.26), residues: 1115 helix: 2.39 (0.24), residues: 411 sheet: -0.56 (0.31), residues: 281 loop : 0.55 (0.33), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 8 TYR 0.021 0.002 TYR S 190 PHE 0.013 0.001 PHE R 147 TRP 0.018 0.001 TRP B 339 HIS 0.003 0.001 HIS R 301 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9059) covalent geometry : angle 0.59381 (12275) SS BOND : bond 0.00140 ( 2) SS BOND : angle 0.22897 ( 4) hydrogen bonds : bond 0.03863 ( 488) hydrogen bonds : angle 4.95014 ( 1380) link_TRANS : bond 0.00150 ( 1) link_TRANS : angle 0.34195 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 73 ASP cc_start: 0.7741 (t0) cc_final: 0.7154 (t0) REVERT: S 85 SER cc_start: 0.9109 (t) cc_final: 0.8860 (p) REVERT: S 89 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7826 (tm-30) REVERT: S 183 GLN cc_start: 0.8280 (mt0) cc_final: 0.7917 (mt0) REVERT: S 192 MET cc_start: 0.8354 (ttp) cc_final: 0.8136 (ttm) REVERT: S 220 GLU cc_start: 0.8383 (pm20) cc_final: 0.7497 (pm20) REVERT: S 222 GLU cc_start: 0.8629 (pt0) cc_final: 0.8300 (pm20) REVERT: S 223 ASP cc_start: 0.8863 (m-30) cc_final: 0.8033 (m-30) REVERT: R 42 ASP cc_start: 0.9062 (m-30) cc_final: 0.8853 (m-30) REVERT: R 114 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8560 (tt0) REVERT: R 191 CYS cc_start: 0.8767 (m) cc_final: 0.8261 (m) REVERT: R 290 ASN cc_start: 0.8503 (t0) cc_final: 0.8220 (t0) REVERT: A 21 GLU cc_start: 0.8533 (tt0) cc_final: 0.8192 (tt0) REVERT: A 236 GLN cc_start: 0.8992 (mt0) cc_final: 0.8732 (mt0) REVERT: A 369 THR cc_start: 0.9218 (p) cc_final: 0.9003 (m) REVERT: A 390 GLN cc_start: 0.9091 (tt0) cc_final: 0.8824 (tt0) REVERT: G 20 LYS cc_start: 0.8290 (ttpp) cc_final: 0.7945 (ptpp) REVERT: B 8 ARG cc_start: 0.8318 (ttp80) cc_final: 0.8088 (tpt90) REVERT: B 10 GLU cc_start: 0.8998 (tp30) cc_final: 0.8531 (tp30) REVERT: B 172 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8041 (mm-30) REVERT: B 217 MET cc_start: 0.8826 (pmm) cc_final: 0.8476 (ppp) REVERT: B 254 ASP cc_start: 0.7972 (t70) cc_final: 0.7585 (t70) REVERT: B 266 HIS cc_start: 0.8541 (OUTLIER) cc_final: 0.8126 (t70) REVERT: B 325 MET cc_start: 0.9006 (tpp) cc_final: 0.8777 (mmm) REVERT: F 11 LYS cc_start: 0.9389 (mttt) cc_final: 0.9086 (mmmm) outliers start: 24 outliers final: 6 residues processed: 162 average time/residue: 0.6707 time to fit residues: 114.6484 Evaluate side-chains 149 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 140 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain R residue 114 GLN Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 23 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 107 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 39 GLN R 91 ASN R 270 HIS A 50 ASN A 59 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.089509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.066956 restraints weight = 17207.286| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.83 r_work: 0.2811 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9062 Z= 0.157 Angle : 0.583 8.394 12282 Z= 0.302 Chirality : 0.042 0.185 1407 Planarity : 0.004 0.052 1554 Dihedral : 4.771 25.738 1242 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.03 % Allowed : 16.08 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.26), residues: 1115 helix: 2.60 (0.24), residues: 409 sheet: -0.51 (0.31), residues: 282 loop : 0.54 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 218 TYR 0.021 0.002 TYR S 190 PHE 0.014 0.001 PHE R 147 TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS R 270 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 9059) covalent geometry : angle 0.58324 (12275) SS BOND : bond 0.00128 ( 2) SS BOND : angle 0.37987 ( 4) hydrogen bonds : bond 0.03748 ( 488) hydrogen bonds : angle 4.82990 ( 1380) link_TRANS : bond 0.00159 ( 1) link_TRANS : angle 0.26844 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 73 ASP cc_start: 0.7756 (t0) cc_final: 0.7209 (t0) REVERT: S 85 SER cc_start: 0.9096 (t) cc_final: 0.8856 (p) REVERT: S 89 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7851 (tm-30) REVERT: S 183 GLN cc_start: 0.8236 (mt0) cc_final: 0.7878 (mt0) REVERT: S 192 MET cc_start: 0.8473 (ttp) cc_final: 0.8234 (ttm) REVERT: S 220 GLU cc_start: 0.8473 (pm20) cc_final: 0.7655 (pm20) REVERT: S 222 GLU cc_start: 0.8629 (pt0) cc_final: 0.8336 (pm20) REVERT: S 223 ASP cc_start: 0.8851 (m-30) cc_final: 0.8141 (m-30) REVERT: R 42 ASP cc_start: 0.9081 (m-30) cc_final: 0.8868 (m-30) REVERT: R 109 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7471 (ptm-80) REVERT: R 191 CYS cc_start: 0.8747 (m) cc_final: 0.8287 (m) REVERT: R 290 ASN cc_start: 0.8532 (t0) cc_final: 0.8250 (t0) REVERT: A 21 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8248 (tt0) REVERT: A 236 GLN cc_start: 0.8983 (mt0) cc_final: 0.8731 (mt0) REVERT: A 369 THR cc_start: 0.9264 (OUTLIER) cc_final: 0.9003 (m) REVERT: G 20 LYS cc_start: 0.8397 (ttpp) cc_final: 0.8194 (ptpp) REVERT: B 10 GLU cc_start: 0.9019 (tp30) cc_final: 0.8557 (tp30) REVERT: B 42 ARG cc_start: 0.7755 (tpt170) cc_final: 0.7505 (tpt170) REVERT: B 172 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8084 (mm-30) REVERT: B 217 MET cc_start: 0.8827 (pmm) cc_final: 0.8501 (ppp) REVERT: B 254 ASP cc_start: 0.7957 (t70) cc_final: 0.7587 (t70) REVERT: B 266 HIS cc_start: 0.8547 (OUTLIER) cc_final: 0.8205 (t70) REVERT: B 325 MET cc_start: 0.8997 (tpp) cc_final: 0.8789 (mmm) REVERT: F 5 GLU cc_start: 0.8181 (pm20) cc_final: 0.7962 (pm20) REVERT: F 11 LYS cc_start: 0.9404 (mttt) cc_final: 0.9120 (mmmm) outliers start: 29 outliers final: 6 residues processed: 166 average time/residue: 0.6775 time to fit residues: 118.8108 Evaluate side-chains 149 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain R residue 109 ARG Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 12 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 4 optimal weight: 0.0980 chunk 107 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 chunk 69 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 39 GLN R 270 HIS ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.088362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.065218 restraints weight = 17433.477| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.86 r_work: 0.2766 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9062 Z= 0.212 Angle : 0.622 8.220 12282 Z= 0.322 Chirality : 0.043 0.207 1407 Planarity : 0.004 0.051 1554 Dihedral : 4.819 23.858 1242 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.71 % Allowed : 16.81 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.26), residues: 1115 helix: 2.54 (0.24), residues: 410 sheet: -0.48 (0.31), residues: 281 loop : 0.46 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 8 TYR 0.023 0.002 TYR S 190 PHE 0.016 0.001 PHE R 147 TRP 0.012 0.001 TRP B 339 HIS 0.005 0.001 HIS R 270 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 9059) covalent geometry : angle 0.62197 (12275) SS BOND : bond 0.00051 ( 2) SS BOND : angle 0.37674 ( 4) hydrogen bonds : bond 0.03871 ( 488) hydrogen bonds : angle 4.87864 ( 1380) link_TRANS : bond 0.00318 ( 1) link_TRANS : angle 0.31742 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 73 ASP cc_start: 0.7732 (t0) cc_final: 0.7153 (t0) REVERT: S 85 SER cc_start: 0.9106 (t) cc_final: 0.8843 (p) REVERT: S 89 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7915 (tm-30) REVERT: S 160 ARG cc_start: 0.8226 (ttm-80) cc_final: 0.8021 (mtp85) REVERT: S 183 GLN cc_start: 0.8298 (mt0) cc_final: 0.7928 (mt0) REVERT: S 192 MET cc_start: 0.8565 (ttp) cc_final: 0.8275 (ttm) REVERT: S 220 GLU cc_start: 0.8495 (pm20) cc_final: 0.7809 (pm20) REVERT: S 222 GLU cc_start: 0.8627 (pt0) cc_final: 0.8306 (pm20) REVERT: S 223 ASP cc_start: 0.8840 (m-30) cc_final: 0.7889 (m-30) REVERT: R 42 ASP cc_start: 0.9107 (m-30) cc_final: 0.8890 (m-30) REVERT: R 65 LYS cc_start: 0.8350 (ttmt) cc_final: 0.7939 (mptt) REVERT: R 84 ASP cc_start: 0.8780 (m-30) cc_final: 0.8457 (t0) REVERT: R 191 CYS cc_start: 0.8725 (m) cc_final: 0.8260 (m) REVERT: R 303 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7982 (tm-30) REVERT: A 21 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8257 (tt0) REVERT: A 236 GLN cc_start: 0.9008 (mt0) cc_final: 0.8709 (mt0) REVERT: A 390 GLN cc_start: 0.9126 (tt0) cc_final: 0.8863 (tt0) REVERT: G 20 LYS cc_start: 0.8342 (ttpp) cc_final: 0.8022 (ptpp) REVERT: B 10 GLU cc_start: 0.8990 (tp30) cc_final: 0.8137 (tp30) REVERT: B 13 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8370 (pp30) REVERT: B 42 ARG cc_start: 0.7823 (tpt170) cc_final: 0.7551 (tpt170) REVERT: B 172 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8101 (mm-30) REVERT: B 217 MET cc_start: 0.8840 (pmm) cc_final: 0.8464 (ppp) REVERT: B 254 ASP cc_start: 0.7984 (t70) cc_final: 0.7583 (t70) REVERT: B 266 HIS cc_start: 0.8574 (OUTLIER) cc_final: 0.8270 (t70) REVERT: F 5 GLU cc_start: 0.8144 (pm20) cc_final: 0.7907 (pm20) REVERT: F 11 LYS cc_start: 0.9395 (mttt) cc_final: 0.9086 (mmmm) outliers start: 26 outliers final: 9 residues processed: 159 average time/residue: 0.6865 time to fit residues: 115.1675 Evaluate side-chains 155 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 153 GLU Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 303 GLN Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 88 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 39 GLN R 270 HIS A 50 ASN A 59 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.088391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.065194 restraints weight = 17162.364| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.85 r_work: 0.2771 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9062 Z= 0.204 Angle : 0.625 8.216 12282 Z= 0.322 Chirality : 0.043 0.195 1407 Planarity : 0.004 0.051 1554 Dihedral : 4.797 21.440 1242 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.61 % Allowed : 17.33 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.26), residues: 1115 helix: 2.56 (0.24), residues: 410 sheet: -0.47 (0.31), residues: 268 loop : 0.36 (0.32), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 8 TYR 0.023 0.002 TYR S 190 PHE 0.015 0.002 PHE R 147 TRP 0.013 0.001 TRP B 339 HIS 0.004 0.001 HIS R 270 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 9059) covalent geometry : angle 0.62538 (12275) SS BOND : bond 0.00124 ( 2) SS BOND : angle 0.37184 ( 4) hydrogen bonds : bond 0.03853 ( 488) hydrogen bonds : angle 4.89722 ( 1380) link_TRANS : bond 0.00296 ( 1) link_TRANS : angle 0.34145 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 73 ASP cc_start: 0.7759 (t0) cc_final: 0.7162 (t0) REVERT: S 85 SER cc_start: 0.9109 (t) cc_final: 0.8842 (p) REVERT: S 89 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7935 (tm-30) REVERT: S 183 GLN cc_start: 0.8324 (mt0) cc_final: 0.7942 (mt0) REVERT: S 192 MET cc_start: 0.8564 (ttp) cc_final: 0.8270 (ttm) REVERT: S 220 GLU cc_start: 0.8512 (pm20) cc_final: 0.7830 (pm20) REVERT: S 222 GLU cc_start: 0.8609 (pt0) cc_final: 0.8300 (pm20) REVERT: S 223 ASP cc_start: 0.8839 (m-30) cc_final: 0.7878 (m-30) REVERT: R 42 ASP cc_start: 0.9108 (m-30) cc_final: 0.8882 (m-30) REVERT: R 65 LYS cc_start: 0.8324 (ttmt) cc_final: 0.7915 (mptt) REVERT: R 109 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7488 (ptt90) REVERT: R 191 CYS cc_start: 0.8736 (m) cc_final: 0.8276 (m) REVERT: R 290 ASN cc_start: 0.8526 (t0) cc_final: 0.8210 (t0) REVERT: A 21 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8264 (tt0) REVERT: A 236 GLN cc_start: 0.8993 (mt0) cc_final: 0.8701 (mt0) REVERT: A 265 ARG cc_start: 0.8949 (mtp85) cc_final: 0.8647 (mtp85) REVERT: A 307 LYS cc_start: 0.9030 (mppt) cc_final: 0.8810 (mppt) REVERT: A 390 GLN cc_start: 0.9147 (tt0) cc_final: 0.8874 (tt0) REVERT: G 20 LYS cc_start: 0.8364 (ttpp) cc_final: 0.8070 (ptpp) REVERT: B 42 ARG cc_start: 0.7764 (tpt170) cc_final: 0.7496 (tpt170) REVERT: B 172 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8095 (mm-30) REVERT: B 217 MET cc_start: 0.8860 (pmm) cc_final: 0.8486 (ppp) REVERT: B 254 ASP cc_start: 0.8007 (t70) cc_final: 0.7600 (t70) REVERT: B 264 TYR cc_start: 0.9191 (m-80) cc_final: 0.8896 (m-80) REVERT: B 325 MET cc_start: 0.9038 (tpp) cc_final: 0.8783 (mmm) REVERT: F 5 GLU cc_start: 0.8154 (pm20) cc_final: 0.7908 (pm20) REVERT: F 11 LYS cc_start: 0.9376 (mttt) cc_final: 0.9089 (mmmm) outliers start: 25 outliers final: 10 residues processed: 157 average time/residue: 0.6699 time to fit residues: 110.9901 Evaluate side-chains 152 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 153 GLU Chi-restraints excluded: chain R residue 109 ARG Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 72 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 50 ASN B 13 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.089822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.066838 restraints weight = 17233.832| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.86 r_work: 0.2812 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9062 Z= 0.148 Angle : 0.614 9.009 12282 Z= 0.316 Chirality : 0.042 0.272 1407 Planarity : 0.004 0.051 1554 Dihedral : 4.729 20.733 1242 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.46 % Allowed : 18.68 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.26), residues: 1115 helix: 2.61 (0.24), residues: 409 sheet: -0.48 (0.31), residues: 276 loop : 0.44 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 8 TYR 0.022 0.002 TYR A 318 PHE 0.013 0.001 PHE A 376 TRP 0.016 0.001 TRP B 339 HIS 0.010 0.001 HIS R 270 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9059) covalent geometry : angle 0.61373 (12275) SS BOND : bond 0.00117 ( 2) SS BOND : angle 0.34758 ( 4) hydrogen bonds : bond 0.03678 ( 488) hydrogen bonds : angle 4.85500 ( 1380) link_TRANS : bond 0.00126 ( 1) link_TRANS : angle 0.28659 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 73 ASP cc_start: 0.7713 (t0) cc_final: 0.7131 (t0) REVERT: S 85 SER cc_start: 0.9084 (t) cc_final: 0.8785 (p) REVERT: S 89 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7928 (tm-30) REVERT: S 183 GLN cc_start: 0.8267 (mt0) cc_final: 0.7906 (mt0) REVERT: S 220 GLU cc_start: 0.8519 (pm20) cc_final: 0.7839 (pm20) REVERT: S 222 GLU cc_start: 0.8621 (pt0) cc_final: 0.8306 (pm20) REVERT: S 223 ASP cc_start: 0.8755 (m-30) cc_final: 0.7896 (m-30) REVERT: R 42 ASP cc_start: 0.9107 (m-30) cc_final: 0.8880 (m-30) REVERT: R 65 LYS cc_start: 0.8336 (ttmt) cc_final: 0.8065 (mptt) REVERT: R 191 CYS cc_start: 0.8724 (m) cc_final: 0.8276 (m) REVERT: A 21 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8242 (tt0) REVERT: A 236 GLN cc_start: 0.8973 (mt0) cc_final: 0.8689 (mt0) REVERT: A 390 GLN cc_start: 0.9106 (tt0) cc_final: 0.8865 (tt0) REVERT: G 17 GLU cc_start: 0.8439 (mm-30) cc_final: 0.7801 (mm-30) REVERT: G 20 LYS cc_start: 0.8369 (ttpp) cc_final: 0.8104 (ptpp) REVERT: B 10 GLU cc_start: 0.9009 (tp30) cc_final: 0.8781 (tp30) REVERT: B 42 ARG cc_start: 0.7797 (tpt170) cc_final: 0.7502 (tpt170) REVERT: B 172 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8127 (mm-30) REVERT: B 217 MET cc_start: 0.8836 (pmm) cc_final: 0.8479 (ppp) REVERT: B 254 ASP cc_start: 0.7950 (t70) cc_final: 0.7540 (t70) REVERT: B 325 MET cc_start: 0.9028 (tpp) cc_final: 0.8753 (mmm) REVERT: F 5 GLU cc_start: 0.8164 (pm20) cc_final: 0.7915 (pm20) REVERT: F 11 LYS cc_start: 0.9375 (mttt) cc_final: 0.9092 (mmmm) outliers start: 14 outliers final: 6 residues processed: 152 average time/residue: 0.7208 time to fit residues: 115.4191 Evaluate side-chains 145 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 110 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 63 optimal weight: 0.0000 chunk 33 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.088491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.065281 restraints weight = 17269.856| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.87 r_work: 0.2779 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9062 Z= 0.200 Angle : 0.655 9.658 12282 Z= 0.337 Chirality : 0.043 0.224 1407 Planarity : 0.004 0.051 1554 Dihedral : 4.787 21.404 1242 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.46 % Allowed : 19.31 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.26), residues: 1115 helix: 2.51 (0.24), residues: 410 sheet: -0.48 (0.31), residues: 274 loop : 0.46 (0.32), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 8 TYR 0.023 0.002 TYR S 190 PHE 0.015 0.002 PHE B 292 TRP 0.012 0.001 TRP B 339 HIS 0.009 0.001 HIS R 270 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 9059) covalent geometry : angle 0.65547 (12275) SS BOND : bond 0.00104 ( 2) SS BOND : angle 0.31810 ( 4) hydrogen bonds : bond 0.03824 ( 488) hydrogen bonds : angle 4.91758 ( 1380) link_TRANS : bond 0.00273 ( 1) link_TRANS : angle 0.28063 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 73 ASP cc_start: 0.7776 (t0) cc_final: 0.7194 (t0) REVERT: S 85 SER cc_start: 0.9100 (t) cc_final: 0.8813 (p) REVERT: S 89 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7949 (tm-30) REVERT: S 183 GLN cc_start: 0.8319 (mt0) cc_final: 0.7968 (mt0) REVERT: S 220 GLU cc_start: 0.8541 (pm20) cc_final: 0.7664 (pm20) REVERT: S 222 GLU cc_start: 0.8597 (pt0) cc_final: 0.8325 (pm20) REVERT: S 223 ASP cc_start: 0.8786 (m-30) cc_final: 0.8156 (m-30) REVERT: R 42 ASP cc_start: 0.9093 (m-30) cc_final: 0.8870 (m-30) REVERT: R 84 ASP cc_start: 0.8823 (m-30) cc_final: 0.8564 (m-30) REVERT: R 115 GLN cc_start: 0.8642 (mm-40) cc_final: 0.8162 (tp40) REVERT: R 191 CYS cc_start: 0.8760 (m) cc_final: 0.8309 (m) REVERT: A 21 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8260 (tt0) REVERT: A 236 GLN cc_start: 0.9039 (mt0) cc_final: 0.8763 (mt0) REVERT: A 368 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.8112 (t0) REVERT: A 390 GLN cc_start: 0.9106 (tt0) cc_final: 0.8859 (tt0) REVERT: G 20 LYS cc_start: 0.8450 (ttpp) cc_final: 0.8181 (ptpp) REVERT: B 10 GLU cc_start: 0.8980 (tp30) cc_final: 0.8138 (pt0) REVERT: B 42 ARG cc_start: 0.7805 (tpt170) cc_final: 0.7506 (tpt170) REVERT: B 172 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8128 (mm-30) REVERT: B 217 MET cc_start: 0.8870 (pmm) cc_final: 0.8142 (ppp) REVERT: B 254 ASP cc_start: 0.8021 (t70) cc_final: 0.7633 (t70) REVERT: B 325 MET cc_start: 0.9050 (tpp) cc_final: 0.8814 (mmm) REVERT: F 5 GLU cc_start: 0.8178 (pm20) cc_final: 0.7926 (pm20) REVERT: F 11 LYS cc_start: 0.9357 (mttt) cc_final: 0.9104 (mmmm) outliers start: 14 outliers final: 8 residues processed: 141 average time/residue: 0.6882 time to fit residues: 102.5711 Evaluate side-chains 144 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 153 GLU Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 301 HIS A 59 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.088298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.065262 restraints weight = 17171.288| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.85 r_work: 0.2773 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9062 Z= 0.200 Angle : 0.651 9.508 12282 Z= 0.335 Chirality : 0.043 0.170 1407 Planarity : 0.004 0.051 1554 Dihedral : 4.786 20.751 1242 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.67 % Allowed : 19.21 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.26), residues: 1115 helix: 2.54 (0.24), residues: 410 sheet: -0.45 (0.31), residues: 268 loop : 0.40 (0.32), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 8 TYR 0.023 0.002 TYR S 190 PHE 0.014 0.001 PHE R 147 TRP 0.013 0.001 TRP B 339 HIS 0.009 0.001 HIS R 270 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 9059) covalent geometry : angle 0.65122 (12275) SS BOND : bond 0.00182 ( 2) SS BOND : angle 0.34919 ( 4) hydrogen bonds : bond 0.03804 ( 488) hydrogen bonds : angle 4.90329 ( 1380) link_TRANS : bond 0.00276 ( 1) link_TRANS : angle 0.31321 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2984.47 seconds wall clock time: 51 minutes 45.03 seconds (3105.03 seconds total)