Starting phenix.real_space_refine on Thu Mar 13 10:47:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f4f_31449/03_2025/7f4f_31449.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f4f_31449/03_2025/7f4f_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_2025/7f4f_31449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f4f_31449/03_2025/7f4f_31449.map" model { file = "/net/cci-nas-00/data/ceres_data/7f4f_31449/03_2025/7f4f_31449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f4f_31449/03_2025/7f4f_31449.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 1} 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: 5.49, per 1000 atoms: 0.62 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: 2.97 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.24 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: 2.72 Time building geometry restraints manager: 2.74 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: 0.470 Set stop_for_unknowns flag: 0.010 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.390 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:13.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.000 ------------------------------------------------------------------------------- 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 9059 Z= 0.629 Angle : 1.093 10.799 12275 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 : 4.69 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (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 TRP 0.043 0.007 TRP B 339 HIS 0.020 0.004 HIS A 387 PHE 0.025 0.005 PHE R 300 TYR 0.039 0.007 TYR B 105 ARG 0.070 0.006 ARG S 191 *********************** 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 : 1.019 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: 0.7737 (mt0) REVERT: A 271 ASN cc_start: 0.7834 (m110) cc_final: 0.7589 (m110) REVERT: A 339 TYR cc_start: 0.7520 (m-80) cc_final: 0.6882 (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: 1.4704 time to fit residues: 354.1389 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 : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 270 HIS A 239 ASN A 294 GLN A 371 ASN 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 = 0.3474 r_free = 0.3474 target = 0.094816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.072762 restraints weight = 16718.361| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.75 r_work: 0.2918 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9059 Z= 0.217 Angle : 0.653 9.044 12275 Z= 0.345 Chirality : 0.044 0.213 1407 Planarity : 0.005 0.052 1554 Dihedral : 6.010 58.808 1242 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.98 % Allowed : 11.38 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.26), residues: 1115 helix: 1.71 (0.25), residues: 410 sheet: -0.47 (0.31), residues: 269 loop : 0.14 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 339 HIS 0.005 0.001 HIS R 225 PHE 0.016 0.002 PHE R 147 TYR 0.015 0.001 TYR S 190 ARG 0.009 0.001 ARG R 151 *********************** 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 186 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: S 73 ASP cc_start: 0.7616 (t0) cc_final: 0.7380 (t0) REVERT: S 85 SER cc_start: 0.9199 (t) cc_final: 0.8981 (p) REVERT: S 89 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7733 (tm-30) REVERT: S 93 MET cc_start: 0.8798 (ttm) cc_final: 0.8591 (tpp) REVERT: S 153 GLU cc_start: 0.7683 (tt0) cc_final: 0.7405 (tt0) REVERT: S 183 GLN cc_start: 0.8278 (mt0) cc_final: 0.7944 (mt0) REVERT: S 220 GLU cc_start: 0.8294 (pm20) cc_final: 0.7615 (pm20) REVERT: S 222 GLU cc_start: 0.8599 (pt0) cc_final: 0.8213 (pm20) REVERT: S 223 ASP cc_start: 0.8815 (m-30) cc_final: 0.7671 (m-30) REVERT: S 234 GLU cc_start: 0.8989 (pt0) cc_final: 0.8667 (pt0) REVERT: R 191 CYS cc_start: 0.8792 (m) cc_final: 0.8293 (m) REVERT: R 215 CYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7953 (t) REVERT: R 294 ASP cc_start: 0.8138 (m-30) cc_final: 0.7666 (m-30) REVERT: A 58 LYS cc_start: 0.8955 (mmmt) cc_final: 0.8751 (mmpt) REVERT: A 236 GLN cc_start: 0.8892 (mt0) cc_final: 0.8674 (mt0) REVERT: A 390 GLN cc_start: 0.8762 (tt0) cc_final: 0.8414 (tt0) REVERT: G 20 LYS cc_start: 0.8654 (ttpp) cc_final: 0.7894 (ptpp) REVERT: B 10 GLU cc_start: 0.8865 (tp30) cc_final: 0.7615 (tp30) REVERT: B 32 GLN cc_start: 0.8986 (mt0) cc_final: 0.8781 (mt0) REVERT: B 172 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7944 (mm-30) REVERT: B 254 ASP cc_start: 0.7959 (t70) cc_final: 0.7587 (t0) REVERT: B 262 MET cc_start: 0.8422 (tpp) cc_final: 0.8096 (ttm) REVERT: B 266 HIS cc_start: 0.8503 (OUTLIER) cc_final: 0.8042 (t70) outliers start: 19 outliers final: 3 residues processed: 174 average time/residue: 1.3842 time to fit residues: 255.2975 Evaluate side-chains 155 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 149 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 109 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 55 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 91 ASN A 267 GLN B 75 GLN 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 = 0.3378 r_free = 0.3378 target = 0.088950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.065777 restraints weight = 17236.055| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.84 r_work: 0.2758 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9059 Z= 0.351 Angle : 0.646 9.395 12275 Z= 0.338 Chirality : 0.045 0.186 1407 Planarity : 0.005 0.050 1554 Dihedral : 5.583 56.653 1242 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.61 % Allowed : 12.94 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.26), residues: 1115 helix: 2.05 (0.24), residues: 405 sheet: -0.55 (0.30), residues: 281 loop : 0.41 (0.33), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 339 HIS 0.005 0.001 HIS B 91 PHE 0.024 0.002 PHE R 147 TYR 0.025 0.002 TYR S 190 ARG 0.007 0.001 ARG B 219 *********************** 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 175 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 73 ASP cc_start: 0.7624 (t0) cc_final: 0.7145 (t0) REVERT: S 85 SER cc_start: 0.9159 (t) cc_final: 0.8896 (p) REVERT: S 89 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7808 (tm-30) REVERT: S 153 GLU cc_start: 0.7862 (tt0) cc_final: 0.7654 (tt0) REVERT: S 183 GLN cc_start: 0.8348 (mt0) cc_final: 0.8001 (mt0) REVERT: S 194 ASN cc_start: 0.9148 (m110) cc_final: 0.8909 (m110) REVERT: S 234 GLU cc_start: 0.8975 (pt0) cc_final: 0.8665 (pt0) REVERT: R 191 CYS cc_start: 0.8797 (m) cc_final: 0.8286 (m) REVERT: R 270 HIS cc_start: 0.8337 (OUTLIER) cc_final: 0.8098 (t-90) REVERT: R 290 ASN cc_start: 0.8538 (t0) cc_final: 0.8170 (t0) REVERT: R 294 ASP cc_start: 0.8236 (m-30) cc_final: 0.7937 (m-30) REVERT: R 303 GLN cc_start: 0.8716 (tp40) cc_final: 0.8514 (tm-30) REVERT: A 21 GLU cc_start: 0.8438 (tt0) cc_final: 0.8118 (tt0) REVERT: A 236 GLN cc_start: 0.9011 (mt0) cc_final: 0.8778 (mt0) REVERT: G 20 LYS cc_start: 0.8274 (ttpp) cc_final: 0.8043 (ptpp) REVERT: G 29 LYS cc_start: 0.8373 (tppt) cc_final: 0.8093 (ttmm) REVERT: B 10 GLU cc_start: 0.8998 (tp30) cc_final: 0.8195 (tp30) REVERT: B 13 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8647 (pp30) REVERT: B 42 ARG cc_start: 0.7645 (tpt170) cc_final: 0.7413 (tpt170) REVERT: B 172 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7989 (mm-30) REVERT: B 254 ASP cc_start: 0.8003 (t70) cc_final: 0.7614 (t70) REVERT: B 262 MET cc_start: 0.8627 (tpp) cc_final: 0.8319 (ttm) REVERT: B 266 HIS cc_start: 0.8561 (OUTLIER) cc_final: 0.8074 (t70) REVERT: B 325 MET cc_start: 0.9037 (tpp) cc_final: 0.8772 (mmm) REVERT: F 11 LYS cc_start: 0.9343 (mmmm) cc_final: 0.9060 (mmmm) outliers start: 25 outliers final: 6 residues processed: 162 average time/residue: 1.4555 time to fit residues: 249.5241 Evaluate side-chains 147 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 83 MET 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 59 GLN Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 153 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 92 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.090440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.067467 restraints weight = 17226.107| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.88 r_work: 0.2797 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9059 Z= 0.204 Angle : 0.581 7.161 12275 Z= 0.305 Chirality : 0.042 0.199 1407 Planarity : 0.004 0.052 1554 Dihedral : 5.291 59.859 1242 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.30 % Allowed : 15.14 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.26), residues: 1115 helix: 2.33 (0.24), residues: 410 sheet: -0.50 (0.31), residues: 279 loop : 0.45 (0.33), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 339 HIS 0.004 0.001 HIS R 301 PHE 0.014 0.001 PHE A 376 TYR 0.019 0.001 TYR S 190 ARG 0.010 0.001 ARG A 265 *********************** 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 168 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: S 73 ASP cc_start: 0.7608 (t0) cc_final: 0.7068 (t0) REVERT: S 85 SER cc_start: 0.9096 (t) cc_final: 0.8825 (p) REVERT: S 89 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7770 (tm-30) REVERT: S 183 GLN cc_start: 0.8226 (mt0) cc_final: 0.7828 (mt0) REVERT: S 220 GLU cc_start: 0.8333 (pm20) cc_final: 0.7657 (pm20) REVERT: S 222 GLU cc_start: 0.8520 (pt0) cc_final: 0.7957 (pp20) REVERT: S 223 ASP cc_start: 0.8872 (m-30) cc_final: 0.7821 (m-30) REVERT: S 234 GLU cc_start: 0.8908 (pt0) cc_final: 0.8646 (pt0) REVERT: R 191 CYS cc_start: 0.8736 (m) cc_final: 0.8246 (m) REVERT: R 303 GLN cc_start: 0.8601 (tp40) cc_final: 0.8346 (tm-30) REVERT: A 21 GLU cc_start: 0.8501 (tt0) cc_final: 0.8163 (tt0) REVERT: A 236 GLN cc_start: 0.9002 (mt0) cc_final: 0.8722 (mt0) REVERT: G 20 LYS cc_start: 0.8242 (ttpp) cc_final: 0.8024 (ptpp) REVERT: B 10 GLU cc_start: 0.8904 (tp30) cc_final: 0.8462 (tp30) REVERT: B 172 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8028 (mm-30) REVERT: B 254 ASP cc_start: 0.7897 (t70) cc_final: 0.7472 (t70) REVERT: B 260 GLU cc_start: 0.8339 (tt0) cc_final: 0.8135 (mt-10) REVERT: B 262 MET cc_start: 0.8585 (tpp) cc_final: 0.8307 (ttm) REVERT: B 266 HIS cc_start: 0.8592 (OUTLIER) cc_final: 0.8156 (t70) REVERT: B 325 MET cc_start: 0.8960 (tpp) cc_final: 0.8739 (mmm) REVERT: F 11 LYS cc_start: 0.9371 (mmmm) cc_final: 0.9080 (mmmm) outliers start: 22 outliers final: 7 residues processed: 160 average time/residue: 1.4201 time to fit residues: 241.1023 Evaluate side-chains 143 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 157 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain G residue 21 MET 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 32 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 overall best weight: 3.2988 ------------------------------------------------------------------------------- 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 270 HIS R 290 ASN A 267 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 = 0.3342 r_free = 0.3342 target = 0.086915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.063358 restraints weight = 17213.747| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.84 r_work: 0.2725 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 9059 Z= 0.450 Angle : 0.674 9.056 12275 Z= 0.346 Chirality : 0.045 0.204 1407 Planarity : 0.005 0.050 1554 Dihedral : 5.404 59.241 1242 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.40 % Allowed : 14.82 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.26), residues: 1115 helix: 2.30 (0.24), residues: 410 sheet: -0.55 (0.31), residues: 279 loop : 0.43 (0.33), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 169 HIS 0.006 0.001 HIS R 209 PHE 0.022 0.002 PHE R 147 TYR 0.027 0.002 TYR S 190 ARG 0.007 0.001 ARG A 265 *********************** 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 162 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 73 ASP cc_start: 0.7835 (t0) cc_final: 0.7217 (t0) REVERT: S 85 SER cc_start: 0.9159 (t) cc_final: 0.8891 (p) REVERT: S 89 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7880 (tm-30) REVERT: S 183 GLN cc_start: 0.8429 (mt0) cc_final: 0.8081 (mt0) REVERT: S 220 GLU cc_start: 0.8280 (pm20) cc_final: 0.7478 (mp0) REVERT: S 222 GLU cc_start: 0.8525 (pt0) cc_final: 0.8243 (pm20) REVERT: S 223 ASP cc_start: 0.8905 (m-30) cc_final: 0.7956 (m-30) REVERT: R 42 ASP cc_start: 0.9081 (m-30) cc_final: 0.8872 (m-30) REVERT: R 65 LYS cc_start: 0.8412 (ttmt) cc_final: 0.8048 (mptt) REVERT: R 191 CYS cc_start: 0.8798 (m) cc_final: 0.8292 (m) REVERT: R 290 ASN cc_start: 0.8564 (t0) cc_final: 0.8233 (t0) REVERT: A 21 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8289 (tt0) REVERT: A 236 GLN cc_start: 0.9109 (mt0) cc_final: 0.8861 (mt0) REVERT: A 390 GLN cc_start: 0.9079 (tt0) cc_final: 0.8806 (tt0) REVERT: G 20 LYS cc_start: 0.8400 (ttpp) cc_final: 0.8082 (ptpp) REVERT: B 8 ARG cc_start: 0.8450 (tpt90) cc_final: 0.8227 (tpt90) REVERT: B 10 GLU cc_start: 0.8962 (tp30) cc_final: 0.8503 (tp30) REVERT: B 42 ARG cc_start: 0.7703 (tpt170) cc_final: 0.7453 (tpt170) REVERT: B 172 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8027 (mm-30) REVERT: B 254 ASP cc_start: 0.8059 (t70) cc_final: 0.7691 (t70) REVERT: B 262 MET cc_start: 0.8681 (tpp) cc_final: 0.8371 (ttm) REVERT: B 266 HIS cc_start: 0.8573 (OUTLIER) cc_final: 0.8222 (t70) REVERT: B 325 MET cc_start: 0.9058 (tpp) cc_final: 0.8845 (mmm) REVERT: F 11 LYS cc_start: 0.9358 (mmmm) cc_final: 0.9102 (mmmm) outliers start: 23 outliers final: 8 residues processed: 155 average time/residue: 1.4723 time to fit residues: 241.4984 Evaluate side-chains 143 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 173 VAL Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain G residue 21 MET 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 44 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 270 HIS A 267 GLN A 278 ASN ** 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 = 0.3367 r_free = 0.3367 target = 0.088177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.066188 restraints weight = 17019.050| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.73 r_work: 0.2785 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9059 Z= 0.261 Angle : 0.605 8.313 12275 Z= 0.311 Chirality : 0.042 0.184 1407 Planarity : 0.004 0.051 1554 Dihedral : 5.172 57.463 1242 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.40 % Allowed : 16.49 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.26), residues: 1115 helix: 2.49 (0.24), residues: 411 sheet: -0.55 (0.31), residues: 281 loop : 0.47 (0.33), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 339 HIS 0.005 0.001 HIS R 270 PHE 0.014 0.001 PHE A 376 TYR 0.023 0.002 TYR S 190 ARG 0.006 0.000 ARG S 218 *********************** 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 169 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 73 ASP cc_start: 0.7810 (t0) cc_final: 0.7233 (t0) REVERT: S 85 SER cc_start: 0.9096 (t) cc_final: 0.8836 (p) REVERT: S 89 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7868 (tm-30) REVERT: S 183 GLN cc_start: 0.8355 (mt0) cc_final: 0.7988 (mt0) REVERT: S 220 GLU cc_start: 0.8282 (pm20) cc_final: 0.7310 (mp0) REVERT: S 222 GLU cc_start: 0.8524 (pt0) cc_final: 0.8226 (pm20) REVERT: S 223 ASP cc_start: 0.8855 (m-30) cc_final: 0.7938 (m-30) REVERT: R 42 ASP cc_start: 0.9068 (m-30) cc_final: 0.8848 (m-30) REVERT: R 191 CYS cc_start: 0.8804 (m) cc_final: 0.8306 (m) REVERT: A 21 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8239 (tt0) REVERT: A 59 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8404 (mm110) REVERT: A 236 GLN cc_start: 0.9050 (mt0) cc_final: 0.8771 (mt0) REVERT: G 20 LYS cc_start: 0.8403 (ttpp) cc_final: 0.8100 (ptpp) REVERT: B 10 GLU cc_start: 0.9011 (tp30) cc_final: 0.8163 (tp30) REVERT: B 13 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8395 (pp30) REVERT: B 172 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8066 (mm-30) REVERT: B 254 ASP cc_start: 0.7991 (t70) cc_final: 0.7618 (t70) REVERT: B 262 MET cc_start: 0.8597 (tpp) cc_final: 0.8367 (ttm) REVERT: B 266 HIS cc_start: 0.8571 (OUTLIER) cc_final: 0.8239 (t70) REVERT: B 325 MET cc_start: 0.9024 (tpp) cc_final: 0.8791 (mmm) REVERT: F 11 LYS cc_start: 0.9376 (mmmm) cc_final: 0.9130 (mmmm) outliers start: 23 outliers final: 9 residues processed: 158 average time/residue: 1.4663 time to fit residues: 244.9387 Evaluate side-chains 145 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 83 MET 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 A residue 21 GLU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain G residue 21 MET 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 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 59 optimal weight: 8.9990 chunk 1 optimal weight: 0.6980 chunk 109 optimal weight: 7.9990 chunk 58 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 76 optimal weight: 0.0670 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 91 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.089959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.068133 restraints weight = 17127.756| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.76 r_work: 0.2836 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9059 Z= 0.192 Angle : 0.601 8.345 12275 Z= 0.308 Chirality : 0.041 0.173 1407 Planarity : 0.004 0.051 1554 Dihedral : 4.931 51.362 1242 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.19 % Allowed : 17.64 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.26), residues: 1115 helix: 2.69 (0.24), residues: 410 sheet: -0.47 (0.31), residues: 282 loop : 0.46 (0.33), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 339 HIS 0.009 0.001 HIS R 270 PHE 0.014 0.001 PHE A 376 TYR 0.021 0.001 TYR S 190 ARG 0.011 0.001 ARG A 265 *********************** 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 172 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 73 ASP cc_start: 0.7736 (t0) cc_final: 0.7194 (t0) REVERT: S 85 SER cc_start: 0.9052 (t) cc_final: 0.8751 (p) REVERT: S 89 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7867 (tm-30) REVERT: S 93 MET cc_start: 0.8617 (tpp) cc_final: 0.8160 (tpp) REVERT: S 183 GLN cc_start: 0.8247 (mt0) cc_final: 0.7900 (mt0) REVERT: S 220 GLU cc_start: 0.8314 (pm20) cc_final: 0.7343 (mp0) REVERT: S 222 GLU cc_start: 0.8525 (pt0) cc_final: 0.8271 (pm20) REVERT: S 223 ASP cc_start: 0.8727 (m-30) cc_final: 0.7883 (m-30) REVERT: R 42 ASP cc_start: 0.9144 (m-30) cc_final: 0.8916 (m-30) REVERT: R 191 CYS cc_start: 0.8765 (m) cc_final: 0.8309 (m) REVERT: A 21 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8219 (tt0) REVERT: A 236 GLN cc_start: 0.9010 (mt0) cc_final: 0.8774 (mt0) REVERT: A 278 ASN cc_start: 0.9254 (m-40) cc_final: 0.8955 (m-40) REVERT: G 20 LYS cc_start: 0.8394 (ttpp) cc_final: 0.8092 (ptpp) REVERT: B 10 GLU cc_start: 0.8941 (tp30) cc_final: 0.7978 (tp30) REVERT: B 13 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8302 (pp30) REVERT: B 42 ARG cc_start: 0.7704 (tpt170) cc_final: 0.7447 (tpt170) REVERT: B 59 TYR cc_start: 0.8628 (m-80) cc_final: 0.8423 (m-80) REVERT: B 172 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8049 (mm-30) REVERT: B 217 MET cc_start: 0.8934 (pmm) cc_final: 0.8710 (pmm) REVERT: B 254 ASP cc_start: 0.7937 (t70) cc_final: 0.7566 (t70) REVERT: B 262 MET cc_start: 0.8527 (tpp) cc_final: 0.8262 (ttm) REVERT: B 266 HIS cc_start: 0.8569 (OUTLIER) cc_final: 0.8265 (t70) REVERT: B 325 MET cc_start: 0.8977 (tpp) cc_final: 0.8775 (mmm) REVERT: F 11 LYS cc_start: 0.9391 (mmmm) cc_final: 0.9099 (mmmm) outliers start: 21 outliers final: 7 residues processed: 162 average time/residue: 1.4304 time to fit residues: 245.1264 Evaluate side-chains 151 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 141 ASP Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 75 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 21 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.085089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.061556 restraints weight = 17867.981| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.90 r_work: 0.2683 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 9059 Z= 0.465 Angle : 0.703 8.503 12275 Z= 0.358 Chirality : 0.045 0.210 1407 Planarity : 0.004 0.051 1554 Dihedral : 5.265 56.914 1242 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.82 % Allowed : 17.75 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.26), residues: 1115 helix: 2.48 (0.25), residues: 411 sheet: -0.47 (0.32), residues: 273 loop : 0.33 (0.32), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 99 HIS 0.007 0.001 HIS R 270 PHE 0.019 0.002 PHE R 147 TYR 0.027 0.002 TYR S 190 ARG 0.008 0.001 ARG A 265 *********************** 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 163 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 73 ASP cc_start: 0.7728 (t0) cc_final: 0.7090 (t0) REVERT: S 85 SER cc_start: 0.9128 (t) cc_final: 0.8825 (p) REVERT: S 89 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7819 (tm-30) REVERT: S 183 GLN cc_start: 0.8481 (mt0) cc_final: 0.8075 (mt0) REVERT: S 220 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: S 222 GLU cc_start: 0.8509 (pt0) cc_final: 0.8200 (pm20) REVERT: S 223 ASP cc_start: 0.8825 (m-30) cc_final: 0.7761 (m-30) REVERT: R 42 ASP cc_start: 0.9086 (m-30) cc_final: 0.8860 (m-30) REVERT: R 65 LYS cc_start: 0.8326 (ttmt) cc_final: 0.7858 (mptt) REVERT: R 84 ASP cc_start: 0.8830 (m-30) cc_final: 0.8456 (t0) REVERT: R 191 CYS cc_start: 0.8730 (m) cc_final: 0.8239 (m) REVERT: A 59 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8324 (mm110) REVERT: A 236 GLN cc_start: 0.9096 (mt0) cc_final: 0.8802 (mt0) REVERT: G 20 LYS cc_start: 0.8484 (ttpp) cc_final: 0.8221 (ptpp) REVERT: G 29 LYS cc_start: 0.8538 (tppt) cc_final: 0.8281 (tppt) REVERT: B 10 GLU cc_start: 0.8964 (tp30) cc_final: 0.8161 (tp30) REVERT: B 13 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8381 (pp30) REVERT: B 42 ARG cc_start: 0.7825 (tpt170) cc_final: 0.7557 (tpt170) REVERT: B 172 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8100 (mm-30) REVERT: B 254 ASP cc_start: 0.8040 (t70) cc_final: 0.7613 (t70) REVERT: B 262 MET cc_start: 0.8725 (tpp) cc_final: 0.8309 (ttm) REVERT: B 325 MET cc_start: 0.9021 (tpp) cc_final: 0.8781 (mmm) REVERT: F 11 LYS cc_start: 0.9412 (mmmm) cc_final: 0.9078 (mmmm) outliers start: 27 outliers final: 7 residues processed: 152 average time/residue: 1.4533 time to fit residues: 233.4590 Evaluate side-chains 146 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 153 GLU Chi-restraints excluded: chain S residue 220 GLU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain G residue 21 MET 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 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 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 75 GLN B 237 ASN ** 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 = 0.3380 r_free = 0.3380 target = 0.088876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.065865 restraints weight = 17006.257| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.82 r_work: 0.2791 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9059 Z= 0.254 Angle : 0.641 9.161 12275 Z= 0.328 Chirality : 0.042 0.174 1407 Planarity : 0.004 0.052 1554 Dihedral : 5.088 53.566 1242 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.26), residues: 1115 helix: 2.67 (0.24), residues: 410 sheet: -0.41 (0.32), residues: 273 loop : 0.36 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 339 HIS 0.009 0.001 HIS R 270 PHE 0.014 0.001 PHE R 147 TYR 0.022 0.002 TYR S 190 ARG 0.008 0.001 ARG S 160 *********************** 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 161 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 73 ASP cc_start: 0.7733 (t0) cc_final: 0.7153 (t0) REVERT: S 85 SER cc_start: 0.9077 (t) cc_final: 0.8757 (p) REVERT: S 89 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7938 (tm-30) REVERT: S 183 GLN cc_start: 0.8337 (mt0) cc_final: 0.7938 (mt0) REVERT: S 220 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: S 222 GLU cc_start: 0.8510 (pt0) cc_final: 0.8270 (pm20) REVERT: S 223 ASP cc_start: 0.8755 (m-30) cc_final: 0.7858 (m-30) REVERT: R 42 ASP cc_start: 0.9075 (m-30) cc_final: 0.8872 (m-30) REVERT: R 65 LYS cc_start: 0.8347 (ttmt) cc_final: 0.8007 (mptt) REVERT: R 191 CYS cc_start: 0.8746 (m) cc_final: 0.8282 (m) REVERT: R 270 HIS cc_start: 0.8581 (OUTLIER) cc_final: 0.8375 (t-170) REVERT: A 236 GLN cc_start: 0.8990 (mt0) cc_final: 0.8730 (mt0) REVERT: G 20 LYS cc_start: 0.8494 (ttpp) cc_final: 0.8253 (ptpp) REVERT: G 46 LYS cc_start: 0.9322 (mtmm) cc_final: 0.9100 (mmmt) REVERT: B 10 GLU cc_start: 0.8947 (tp30) cc_final: 0.7987 (tp30) REVERT: B 13 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8286 (pp30) REVERT: B 42 ARG cc_start: 0.7789 (tpt170) cc_final: 0.7506 (tpt170) REVERT: B 59 TYR cc_start: 0.8638 (m-80) cc_final: 0.8051 (m-80) REVERT: B 75 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7476 (mt0) REVERT: B 172 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8132 (mm-30) REVERT: B 217 MET cc_start: 0.9007 (pmm) cc_final: 0.8721 (pmm) REVERT: B 254 ASP cc_start: 0.7987 (t70) cc_final: 0.7599 (t70) REVERT: B 260 GLU cc_start: 0.8247 (tt0) cc_final: 0.7986 (mm-30) REVERT: B 262 MET cc_start: 0.8617 (tpp) cc_final: 0.8407 (ttm) REVERT: B 292 PHE cc_start: 0.8723 (m-10) cc_final: 0.8482 (m-10) REVERT: B 325 MET cc_start: 0.8995 (tpp) cc_final: 0.8754 (mmm) REVERT: F 11 LYS cc_start: 0.9431 (mmmm) cc_final: 0.9120 (mmmm) outliers start: 16 outliers final: 7 residues processed: 153 average time/residue: 1.3978 time to fit residues: 226.2777 Evaluate side-chains 149 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 153 GLU Chi-restraints excluded: chain S residue 220 GLU Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain R residue 270 HIS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 75 GLN 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 25 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 75 GLN ** 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 = 0.3365 r_free = 0.3365 target = 0.088598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.065489 restraints weight = 17303.972| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.87 r_work: 0.2774 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9059 Z= 0.245 Angle : 0.644 9.407 12275 Z= 0.329 Chirality : 0.043 0.229 1407 Planarity : 0.004 0.051 1554 Dihedral : 5.017 50.309 1242 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.15 % Allowed : 20.15 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.26), residues: 1115 helix: 2.73 (0.24), residues: 410 sheet: -0.42 (0.32), residues: 273 loop : 0.37 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 339 HIS 0.010 0.001 HIS R 270 PHE 0.013 0.001 PHE A 376 TYR 0.021 0.002 TYR S 190 ARG 0.013 0.001 ARG B 8 ********************** 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 148 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 73 ASP cc_start: 0.7610 (t0) cc_final: 0.7025 (t0) REVERT: S 85 SER cc_start: 0.9055 (t) cc_final: 0.8717 (p) REVERT: S 89 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7912 (tm-30) REVERT: S 183 GLN cc_start: 0.8313 (mt0) cc_final: 0.7925 (mt0) REVERT: S 220 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7252 (mp0) REVERT: S 222 GLU cc_start: 0.8486 (pt0) cc_final: 0.8253 (pm20) REVERT: S 223 ASP cc_start: 0.8707 (m-30) cc_final: 0.7757 (m-30) REVERT: R 42 ASP cc_start: 0.9081 (m-30) cc_final: 0.8855 (m-30) REVERT: R 115 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8174 (tp40) REVERT: R 191 CYS cc_start: 0.8714 (m) cc_final: 0.8259 (m) REVERT: G 20 LYS cc_start: 0.8486 (ttpp) cc_final: 0.8254 (ptpp) REVERT: G 46 LYS cc_start: 0.9340 (mtmm) cc_final: 0.9121 (mmmt) REVERT: G 58 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8375 (mp0) REVERT: B 10 GLU cc_start: 0.8942 (tp30) cc_final: 0.7985 (tp30) REVERT: B 13 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8307 (pp30) REVERT: B 59 TYR cc_start: 0.8545 (m-80) cc_final: 0.8235 (m-80) REVERT: B 172 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8185 (mm-30) REVERT: B 217 MET cc_start: 0.8991 (pmm) cc_final: 0.8717 (pmm) REVERT: B 254 ASP cc_start: 0.7938 (t70) cc_final: 0.7521 (t70) REVERT: B 260 GLU cc_start: 0.8270 (tt0) cc_final: 0.7984 (mm-30) REVERT: B 262 MET cc_start: 0.8614 (tpp) cc_final: 0.8332 (ttm) REVERT: F 11 LYS cc_start: 0.9428 (mmmm) cc_final: 0.9100 (mmmm) outliers start: 11 outliers final: 6 residues processed: 143 average time/residue: 1.4118 time to fit residues: 214.3014 Evaluate side-chains 144 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 220 GLU Chi-restraints excluded: chain R residue 173 VAL Chi-restraints excluded: chain G residue 21 MET 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 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 101 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 62 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 79 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 75 GLN ** 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 = 0.3369 r_free = 0.3369 target = 0.088399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.065306 restraints weight = 17310.219| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.85 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: 0.8276 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9059 Z= 0.284 Angle : 0.644 8.917 12275 Z= 0.330 Chirality : 0.043 0.161 1407 Planarity : 0.004 0.051 1554 Dihedral : 5.063 54.858 1242 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.36 % Allowed : 20.67 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.26), residues: 1115 helix: 2.60 (0.25), residues: 411 sheet: -0.41 (0.32), residues: 273 loop : 0.34 (0.32), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 339 HIS 0.004 0.001 HIS R 301 PHE 0.015 0.001 PHE R 147 TYR 0.020 0.002 TYR A 318 ARG 0.010 0.001 ARG S 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6560.19 seconds wall clock time: 114 minutes 3.92 seconds (6843.92 seconds total)