Starting phenix.real_space_refine on Thu Mar 13 16:39:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h0q_34414/03_2025/8h0q_34414.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h0q_34414/03_2025/8h0q_34414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h0q_34414/03_2025/8h0q_34414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h0q_34414/03_2025/8h0q_34414.map" model { file = "/net/cci-nas-00/data/ceres_data/8h0q_34414/03_2025/8h0q_34414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h0q_34414/03_2025/8h0q_34414.cif" } resolution = 3.3 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= 0.002 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: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5730 2.51 5 N 1520 2.21 5 O 1641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 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: 8949 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2356 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 281} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 74 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "A" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1705 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 202} Chain breaks: 4 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2576 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1753 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "G" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 401 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 50} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.95, per 1000 atoms: 0.66 Number of scatterers: 8949 At special positions: 0 Unit cell: (122.4, 92.8, 128, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1641 8.00 N 1520 7.00 C 5730 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 113 " - pdb=" SG CYS R 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 1.1 seconds 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 14 sheets defined 36.5% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'R' and resid 42 through 68 Processing helix chain 'R' and resid 73 through 102 removed outlier: 3.558A pdb=" N LEU R 77 " --> pdb=" O ASN R 73 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE R 78 " --> pdb=" O VAL R 74 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE R 79 " --> pdb=" O PRO R 75 " (cutoff:3.500A) Proline residue: R 95 - end of helix Processing helix chain 'R' and resid 111 through 142 removed outlier: 3.643A pdb=" N LEU R 115 " --> pdb=" O ILE R 111 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE R 116 " --> pdb=" O GLY R 112 " (cutoff:3.500A) Proline residue: R 117 - end of helix removed outlier: 3.730A pdb=" N GLN R 120 " --> pdb=" O ILE R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 178 removed outlier: 3.589A pdb=" N CYS R 158 " --> pdb=" O LEU R 154 " (cutoff:3.500A) Proline residue: R 174 - end of helix Processing helix chain 'R' and resid 204 through 219 removed outlier: 3.843A pdb=" N LYS R 208 " --> pdb=" O GLU R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 241 Processing helix chain 'R' and resid 249 through 290 Proline residue: R 279 - end of helix Processing helix chain 'R' and resid 297 through 318 removed outlier: 3.921A pdb=" N SER R 315 " --> pdb=" O ALA R 311 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 326 Processing helix chain 'R' and resid 329 through 339 removed outlier: 4.046A pdb=" N LEU R 337 " --> pdb=" O PHE R 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.555A pdb=" N VAL A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 59 Processing helix chain 'A' and resid 215 through 221 removed outlier: 3.563A pdb=" N GLN A 218 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 260 Processing helix chain 'A' and resid 261 through 265 removed outlier: 3.824A pdb=" N ARG A 265 " --> pdb=" O ARG A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 284 Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 308 through 318 Processing helix chain 'A' and resid 335 through 356 Processing helix chain 'B' and resid 9 through 30 Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.580A pdb=" N ILE B 38 " --> pdb=" O THR B 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 28 through 43 removed outlier: 3.645A pdb=" N ALA G 32 " --> pdb=" O LYS G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 58 Processing sheet with id=AA1, first strand: chain 'R' and resid 180 through 181 Processing sheet with id=AA2, first strand: chain 'A' and resid 189 through 196 removed outlier: 6.269A pdb=" N LEU A 40 " --> pdb=" O HIS A 202 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N PHE A 204 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU A 42 " --> pdb=" O PHE A 204 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N VAL A 206 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LEU A 44 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA A 225 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL A 269 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N HIS A 327 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU A 271 " --> pdb=" O HIS A 327 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 56 removed outlier: 3.839A pdb=" N ARG B 54 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 56 " --> pdb=" O LEU B 341 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 63 through 67 removed outlier: 7.052A pdb=" N ALA B 78 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N MET B 66 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL B 76 " --> pdb=" O MET B 66 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER B 79 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASP B 88 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LYS B 94 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.981A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS B 119 " --> pdb=" O SER B 127 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY B 121 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 161 through 165 removed outlier: 3.933A pdb=" N THR B 183 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 194 through 197 removed outlier: 3.826A pdb=" N SER B 194 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 234 through 239 removed outlier: 6.635A pdb=" N CYS B 255 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR B 268 " --> pdb=" O CYS B 255 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU B 257 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 278 through 283 removed outlier: 4.026A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA B 292 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN B 300 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY B 311 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 2 through 6 removed outlier: 3.690A pdb=" N ARG E 17 " --> pdb=" O MET E 82 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET E 82 " --> pdb=" O ARG E 17 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 9 through 11 Processing sheet with id=AB3, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.931A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 155 through 160 Processing sheet with id=AB5, first strand: chain 'E' and resid 176 through 178 removed outlier: 6.811A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1185 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: 2.79 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.87 - 1.06: 3 1.06 - 1.26: 1436 1.26 - 1.46: 2822 1.46 - 1.65: 4789 1.65 - 1.85: 95 Bond restraints: 9145 Sorted by residual: bond pdb=" C13 CLR R 401 " pdb=" C17 CLR R 401 " ideal model delta sigma weight residual 1.550 0.868 0.682 2.00e-02 2.50e+03 1.16e+03 bond pdb=" C13 CLR R 402 " pdb=" C17 CLR R 402 " ideal model delta sigma weight residual 1.550 0.869 0.681 2.00e-02 2.50e+03 1.16e+03 bond pdb=" C13 CLR R 403 " pdb=" C17 CLR R 403 " ideal model delta sigma weight residual 1.550 0.870 0.680 2.00e-02 2.50e+03 1.16e+03 bond pdb=" C15 CLR R 403 " pdb=" C16 CLR R 403 " ideal model delta sigma weight residual 1.541 1.166 0.375 2.00e-02 2.50e+03 3.51e+02 bond pdb=" C15 CLR R 402 " pdb=" C16 CLR R 402 " ideal model delta sigma weight residual 1.541 1.167 0.374 2.00e-02 2.50e+03 3.50e+02 ... (remaining 9140 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 12305 2.44 - 4.88: 87 4.88 - 7.31: 7 7.31 - 9.75: 3 9.75 - 12.19: 9 Bond angle restraints: 12411 Sorted by residual: angle pdb=" C5 CLR R 401 " pdb=" C6 CLR R 401 " pdb=" C7 CLR R 401 " ideal model delta sigma weight residual 125.11 112.92 12.19 3.00e+00 1.11e-01 1.65e+01 angle pdb=" C4 CLR R 402 " pdb=" C5 CLR R 402 " pdb=" C6 CLR R 402 " ideal model delta sigma weight residual 120.33 108.32 12.01 3.00e+00 1.11e-01 1.60e+01 angle pdb=" C5 CLR R 403 " pdb=" C6 CLR R 403 " pdb=" C7 CLR R 403 " ideal model delta sigma weight residual 125.11 113.12 11.99 3.00e+00 1.11e-01 1.60e+01 angle pdb=" C5 CLR R 402 " pdb=" C6 CLR R 402 " pdb=" C7 CLR R 402 " ideal model delta sigma weight residual 125.11 113.22 11.89 3.00e+00 1.11e-01 1.57e+01 angle pdb=" C4 CLR R 403 " pdb=" C5 CLR R 403 " pdb=" C6 CLR R 403 " ideal model delta sigma weight residual 120.33 108.45 11.88 3.00e+00 1.11e-01 1.57e+01 ... (remaining 12406 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.99: 5260 12.99 - 25.98: 191 25.98 - 38.97: 84 38.97 - 51.97: 20 51.97 - 64.96: 15 Dihedral angle restraints: 5570 sinusoidal: 2267 harmonic: 3303 Sorted by residual: dihedral pdb=" CA CYS E 95 " pdb=" C CYS E 95 " pdb=" N VAL E 96 " pdb=" CA VAL E 96 " ideal model delta harmonic sigma weight residual -180.00 -155.79 -24.21 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" N ARG B 288 " pdb=" CA ARG B 288 " pdb=" CB ARG B 288 " pdb=" CG ARG B 288 " ideal model delta sinusoidal sigma weight residual -60.00 -117.26 57.26 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CA LYS R 331 " pdb=" CB LYS R 331 " pdb=" CG LYS R 331 " pdb=" CD LYS R 331 " ideal model delta sinusoidal sigma weight residual -60.00 -111.39 51.39 3 1.50e+01 4.44e-03 9.01e+00 ... (remaining 5567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.328: 1414 0.328 - 0.656: 3 0.656 - 0.985: 0 0.985 - 1.313: 0 1.313 - 1.641: 3 Chirality restraints: 1420 Sorted by residual: chirality pdb=" C13 CLR R 401 " pdb=" C12 CLR R 401 " pdb=" C14 CLR R 401 " pdb=" C17 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.93 -1.29 -1.64 2.00e-01 2.50e+01 6.73e+01 chirality pdb=" C13 CLR R 402 " pdb=" C12 CLR R 402 " pdb=" C14 CLR R 402 " pdb=" C17 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.93 -1.29 -1.64 2.00e-01 2.50e+01 6.71e+01 chirality pdb=" C13 CLR R 403 " pdb=" C12 CLR R 403 " pdb=" C14 CLR R 403 " pdb=" C17 CLR R 403 " both_signs ideal model delta sigma weight residual False -2.93 -1.30 -1.64 2.00e-01 2.50e+01 6.70e+01 ... (remaining 1417 not shown) Planarity restraints: 1551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS E 95 " -0.021 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C CYS E 95 " 0.071 2.00e-02 2.50e+03 pdb=" O CYS E 95 " -0.027 2.00e-02 2.50e+03 pdb=" N VAL E 96 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 125 " -0.006 2.00e-02 2.50e+03 1.21e-02 1.46e+00 pdb=" C GLY R 125 " 0.021 2.00e-02 2.50e+03 pdb=" O GLY R 125 " -0.008 2.00e-02 2.50e+03 pdb=" N VAL R 126 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 126 " 0.006 2.00e-02 2.50e+03 1.19e-02 1.42e+00 pdb=" C VAL R 126 " -0.021 2.00e-02 2.50e+03 pdb=" O VAL R 126 " 0.008 2.00e-02 2.50e+03 pdb=" N SER R 127 " 0.007 2.00e-02 2.50e+03 ... (remaining 1548 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2030 2.79 - 3.32: 8363 3.32 - 3.84: 14483 3.84 - 4.37: 16305 4.37 - 4.90: 28841 Nonbonded interactions: 70022 Sorted by model distance: nonbonded pdb=" OG SER B 336 " pdb=" OD1 ASP B 338 " model vdw 2.260 3.040 nonbonded pdb=" OG SER R 258 " pdb=" O VAL A 359 " model vdw 2.286 3.040 nonbonded pdb=" OH TYR R 199 " pdb=" OH TYR R 284 " model vdw 2.307 3.040 nonbonded pdb=" O ARG A 338 " pdb=" ND2 ASN A 342 " model vdw 2.330 3.120 nonbonded pdb=" OG1 THR R 296 " pdb=" OD1 ASN L 19 " model vdw 2.340 3.040 ... (remaining 70017 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 24.760 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 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 : 0.019 0.682 9145 Z= 1.288 Angle : 0.589 12.188 12411 Z= 0.281 Chirality : 0.090 1.641 1420 Planarity : 0.003 0.041 1551 Dihedral : 9.284 64.956 3426 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.62 % Allowed : 4.89 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.23), residues: 1110 helix: 0.32 (0.25), residues: 375 sheet: -1.81 (0.28), residues: 254 loop : -2.29 (0.24), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 174 HIS 0.002 0.000 HIS A 322 PHE 0.006 0.001 PHE R 118 TYR 0.005 0.000 TYR E 101 ARG 0.001 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 412 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 90 LEU cc_start: 0.8393 (mt) cc_final: 0.8147 (mt) REVERT: R 205 LEU cc_start: 0.9178 (tp) cc_final: 0.8972 (tt) REVERT: A 34 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7776 (tp40) REVERT: A 58 GLN cc_start: 0.7779 (mm-40) cc_final: 0.7450 (mm-40) REVERT: A 315 ASP cc_start: 0.7476 (t70) cc_final: 0.7254 (t0) REVERT: B 17 GLU cc_start: 0.9244 (tp30) cc_final: 0.9009 (tp30) REVERT: B 83 LYS cc_start: 0.7678 (mmtt) cc_final: 0.7471 (mmtm) REVERT: B 193 MET cc_start: 0.8421 (mmm) cc_final: 0.8084 (mmt) REVERT: B 203 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8780 (pp) REVERT: B 223 CYS cc_start: 0.7283 (p) cc_final: 0.6985 (t) REVERT: B 285 LYS cc_start: 0.8330 (ttpt) cc_final: 0.8081 (ttmm) REVERT: E 13 PRO cc_start: 0.8924 (Cg_endo) cc_final: 0.8217 (Cg_exo) REVERT: E 45 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7806 (mt-10) REVERT: E 52 SER cc_start: 0.8375 (p) cc_final: 0.7683 (t) REVERT: E 67 PHE cc_start: 0.7555 (m-80) cc_final: 0.7311 (m-80) REVERT: E 90 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8368 (t) REVERT: E 206 SER cc_start: 0.8344 (t) cc_final: 0.7979 (p) REVERT: G 13 LYS cc_start: 0.8892 (ptpp) cc_final: 0.8394 (mtpp) REVERT: G 15 VAL cc_start: 0.9560 (p) cc_final: 0.9286 (p) REVERT: G 31 LYS cc_start: 0.9279 (tttp) cc_final: 0.8638 (tptm) outliers start: 6 outliers final: 2 residues processed: 418 average time/residue: 0.2826 time to fit residues: 151.2415 Evaluate side-chains 241 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 237 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain E residue 90 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 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 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 120 GLN ** R 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 341 GLN ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 ASN A 322 HIS A 357 ASN B 59 HIS B 67 HIS B 93 ASN B 96 HIS B 316 HIS E 76 ASN ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.131531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.103917 restraints weight = 16924.965| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 3.21 r_work: 0.3386 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9145 Z= 0.261 Angle : 0.611 5.862 12411 Z= 0.312 Chirality : 0.043 0.164 1420 Planarity : 0.004 0.036 1551 Dihedral : 6.641 57.511 1425 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.68 % Allowed : 15.18 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.25), residues: 1110 helix: 1.67 (0.27), residues: 376 sheet: -1.61 (0.29), residues: 264 loop : -1.60 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 21 HIS 0.005 0.001 HIS E 34 PHE 0.018 0.002 PHE R 275 TYR 0.014 0.001 TYR R 199 ARG 0.006 0.001 ARG E 191 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 255 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 61 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8231 (tt) REVERT: R 82 LEU cc_start: 0.8084 (tp) cc_final: 0.7804 (tt) REVERT: R 205 LEU cc_start: 0.9210 (tp) cc_final: 0.8950 (tt) REVERT: R 212 MET cc_start: 0.7958 (tpp) cc_final: 0.6582 (ttt) REVERT: R 286 TYR cc_start: 0.8232 (t80) cc_final: 0.7721 (t80) REVERT: R 295 ASP cc_start: 0.7538 (p0) cc_final: 0.7039 (p0) REVERT: L 26 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6799 (pp) REVERT: A 24 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7679 (mtm) REVERT: A 26 GLU cc_start: 0.8249 (tp30) cc_final: 0.7950 (mm-30) REVERT: A 28 GLN cc_start: 0.8402 (tp40) cc_final: 0.8162 (tp40) REVERT: A 34 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7988 (mm-40) REVERT: A 249 GLN cc_start: 0.8810 (tp40) cc_final: 0.8580 (tp40) REVERT: B 203 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8787 (pp) REVERT: B 220 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8359 (pm20) REVERT: B 285 LYS cc_start: 0.8603 (ttpt) cc_final: 0.8372 (ttmm) REVERT: B 340 PHE cc_start: 0.8219 (m-10) cc_final: 0.7911 (m-10) REVERT: B 344 TRP cc_start: 0.8803 (m100) cc_final: 0.8486 (m-10) REVERT: E 2 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7697 (mm-40) REVERT: E 45 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8324 (mt-10) REVERT: E 52 SER cc_start: 0.8331 (p) cc_final: 0.8087 (t) REVERT: E 72 ASP cc_start: 0.7309 (t70) cc_final: 0.6738 (p0) REVERT: E 90 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8438 (t) REVERT: E 107 PHE cc_start: 0.8892 (m-80) cc_final: 0.8583 (m-80) REVERT: E 138 ILE cc_start: 0.8423 (mm) cc_final: 0.8209 (mm) REVERT: E 165 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7475 (pp) REVERT: E 202 ARG cc_start: 0.6957 (mtm110) cc_final: 0.6654 (mtm180) REVERT: E 220 GLU cc_start: 0.8174 (mp0) cc_final: 0.7714 (mp0) REVERT: E 223 ASP cc_start: 0.8917 (p0) cc_final: 0.8371 (p0) REVERT: E 228 TYR cc_start: 0.8361 (m-80) cc_final: 0.8095 (m-80) REVERT: G 12 ARG cc_start: 0.8910 (ptp-170) cc_final: 0.8531 (ptp90) REVERT: G 31 LYS cc_start: 0.9111 (tttp) cc_final: 0.8739 (tptm) REVERT: G 35 ASP cc_start: 0.8681 (m-30) cc_final: 0.8196 (m-30) outliers start: 45 outliers final: 24 residues processed: 286 average time/residue: 0.2081 time to fit residues: 81.6368 Evaluate side-chains 242 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 211 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 92 THR Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 299 LEU Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain G residue 25 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 65 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 72 optimal weight: 0.0020 chunk 37 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 96 optimal weight: 0.3980 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 332 GLN ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 HIS ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.128562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.102297 restraints weight = 17446.104| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 3.16 r_work: 0.3356 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.5042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9145 Z= 0.177 Angle : 0.542 7.101 12411 Z= 0.276 Chirality : 0.042 0.169 1420 Planarity : 0.003 0.038 1551 Dihedral : 5.970 54.459 1425 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.89 % Allowed : 16.22 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.25), residues: 1110 helix: 1.96 (0.28), residues: 386 sheet: -1.43 (0.30), residues: 253 loop : -1.55 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 21 HIS 0.003 0.001 HIS R 206 PHE 0.023 0.001 PHE R 275 TYR 0.017 0.001 TYR R 199 ARG 0.006 0.001 ARG A 297 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 225 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 61 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8315 (tt) REVERT: R 82 LEU cc_start: 0.8099 (tp) cc_final: 0.7829 (tt) REVERT: R 205 LEU cc_start: 0.9192 (tp) cc_final: 0.8922 (tt) REVERT: R 286 TYR cc_start: 0.8208 (t80) cc_final: 0.7794 (t80) REVERT: R 293 GLU cc_start: 0.8168 (pm20) cc_final: 0.7868 (pm20) REVERT: R 295 ASP cc_start: 0.7569 (p0) cc_final: 0.7329 (p0) REVERT: L 26 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.7075 (pp) REVERT: A 24 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7693 (mtm) REVERT: A 28 GLN cc_start: 0.8480 (tp40) cc_final: 0.8175 (tp40) REVERT: A 249 GLN cc_start: 0.8850 (tp40) cc_final: 0.8594 (tp40) REVERT: A 315 ASP cc_start: 0.8297 (m-30) cc_final: 0.8080 (m-30) REVERT: B 203 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8833 (pp) REVERT: B 220 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8389 (pm20) REVERT: B 302 TRP cc_start: 0.8939 (m100) cc_final: 0.8608 (m-10) REVERT: B 334 THR cc_start: 0.9312 (m) cc_final: 0.8863 (p) REVERT: B 340 PHE cc_start: 0.8244 (m-10) cc_final: 0.7989 (m-10) REVERT: E 72 ASP cc_start: 0.6933 (t70) cc_final: 0.6630 (t70) REVERT: E 82 MET cc_start: 0.7559 (pmm) cc_final: 0.7289 (ptp) REVERT: E 90 THR cc_start: 0.8648 (OUTLIER) cc_final: 0.8291 (t) REVERT: E 138 ILE cc_start: 0.8277 (mm) cc_final: 0.7862 (mm) REVERT: E 140 MET cc_start: 0.7676 (pmm) cc_final: 0.7453 (pmm) REVERT: E 165 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7708 (pp) REVERT: E 179 GLN cc_start: 0.8031 (tm-30) cc_final: 0.7736 (tm-30) REVERT: E 218 ARG cc_start: 0.8168 (mmp80) cc_final: 0.7941 (mmp80) REVERT: E 223 ASP cc_start: 0.8976 (p0) cc_final: 0.8533 (p0) REVERT: G 12 ARG cc_start: 0.8875 (ptp-170) cc_final: 0.8382 (ptp90) REVERT: G 13 LYS cc_start: 0.8973 (ptpp) cc_final: 0.8750 (mmtm) REVERT: G 28 LYS cc_start: 0.8773 (mmmm) cc_final: 0.8500 (tptp) REVERT: G 31 LYS cc_start: 0.9134 (tttp) cc_final: 0.8724 (tptm) REVERT: G 35 ASP cc_start: 0.8711 (m-30) cc_final: 0.8117 (m-30) outliers start: 47 outliers final: 26 residues processed: 255 average time/residue: 0.1988 time to fit residues: 71.6669 Evaluate side-chains 236 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 76 ASN Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 283 ILE Chi-restraints excluded: chain R residue 299 LEU Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain G residue 25 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 41 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 95 optimal weight: 40.0000 chunk 96 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 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 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN G 43 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.125226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.098448 restraints weight = 17186.528| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 3.31 r_work: 0.3281 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9145 Z= 0.209 Angle : 0.559 7.460 12411 Z= 0.285 Chirality : 0.042 0.184 1420 Planarity : 0.003 0.038 1551 Dihedral : 5.761 53.443 1425 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.61 % Allowed : 17.05 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.26), residues: 1110 helix: 2.02 (0.28), residues: 390 sheet: -1.41 (0.30), residues: 263 loop : -1.39 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP L 21 HIS 0.006 0.001 HIS B 147 PHE 0.028 0.001 PHE R 275 TYR 0.016 0.001 TYR R 199 ARG 0.005 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 215 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 61 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8300 (tt) REVERT: R 82 LEU cc_start: 0.8212 (tp) cc_final: 0.7981 (tt) REVERT: R 205 LEU cc_start: 0.9205 (tp) cc_final: 0.8930 (tt) REVERT: R 212 MET cc_start: 0.8142 (tpp) cc_final: 0.6672 (ttt) REVERT: R 286 TYR cc_start: 0.8305 (t80) cc_final: 0.7822 (t80) REVERT: R 293 GLU cc_start: 0.8289 (pm20) cc_final: 0.7966 (pm20) REVERT: L 26 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7096 (pp) REVERT: A 253 ASN cc_start: 0.9266 (OUTLIER) cc_final: 0.8552 (m110) REVERT: A 315 ASP cc_start: 0.8350 (m-30) cc_final: 0.8112 (m-30) REVERT: B 176 ILE cc_start: 0.8354 (mt) cc_final: 0.8132 (pt) REVERT: B 203 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8838 (pp) REVERT: B 220 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8393 (pm20) REVERT: B 334 THR cc_start: 0.9332 (m) cc_final: 0.8960 (p) REVERT: B 344 TRP cc_start: 0.8811 (m100) cc_final: 0.8447 (m-10) REVERT: E 2 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7673 (mm-40) REVERT: E 90 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.8316 (t) REVERT: E 138 ILE cc_start: 0.8297 (mm) cc_final: 0.7825 (mm) REVERT: E 140 MET cc_start: 0.7795 (pmm) cc_final: 0.7575 (pmm) REVERT: E 160 ARG cc_start: 0.8219 (mtm-85) cc_final: 0.7974 (mtm-85) REVERT: E 165 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7729 (pp) REVERT: G 12 ARG cc_start: 0.8833 (ptp-170) cc_final: 0.8489 (ptp90) REVERT: G 28 LYS cc_start: 0.8786 (mmmm) cc_final: 0.8498 (tptp) REVERT: G 31 LYS cc_start: 0.9174 (tttp) cc_final: 0.8762 (tptm) REVERT: G 35 ASP cc_start: 0.8777 (m-30) cc_final: 0.8212 (m-30) REVERT: G 47 ASP cc_start: 0.8699 (t0) cc_final: 0.8370 (t0) outliers start: 54 outliers final: 34 residues processed: 246 average time/residue: 0.1870 time to fit residues: 65.2125 Evaluate side-chains 243 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 202 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 76 ASN Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 175 GLU Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 283 ILE Chi-restraints excluded: chain R residue 299 LEU Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 CYS Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain G residue 25 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 79 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 chunk 106 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 120 GLN ** R 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.112507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.084189 restraints weight = 17046.872| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 3.11 r_work: 0.3028 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.7257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.076 9145 Z= 0.645 Angle : 0.816 8.817 12411 Z= 0.424 Chirality : 0.051 0.257 1420 Planarity : 0.005 0.053 1551 Dihedral : 6.345 58.604 1424 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 7.28 % Allowed : 16.84 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.25), residues: 1110 helix: 1.21 (0.26), residues: 382 sheet: -1.52 (0.29), residues: 271 loop : -1.29 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 21 HIS 0.009 0.002 HIS B 147 PHE 0.023 0.002 PHE E 212 TYR 0.030 0.002 TYR R 199 ARG 0.005 0.001 ARG R 144 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 187 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 61 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8223 (tt) REVERT: R 97 ASP cc_start: 0.8626 (t0) cc_final: 0.8310 (t70) REVERT: R 205 LEU cc_start: 0.9348 (tp) cc_final: 0.9084 (tt) REVERT: R 239 GLN cc_start: 0.8657 (tp40) cc_final: 0.8313 (tm-30) REVERT: R 286 TYR cc_start: 0.8550 (t80) cc_final: 0.8275 (t80) REVERT: R 295 ASP cc_start: 0.7922 (p0) cc_final: 0.7373 (p0) REVERT: A 28 GLN cc_start: 0.8930 (tp40) cc_final: 0.8660 (tp40) REVERT: A 30 GLN cc_start: 0.8586 (tt0) cc_final: 0.8103 (tp-100) REVERT: A 209 GLN cc_start: 0.7432 (mm-40) cc_final: 0.7218 (mm-40) REVERT: B 203 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8839 (pp) REVERT: B 220 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8282 (pm20) REVERT: B 344 TRP cc_start: 0.9006 (m100) cc_final: 0.8526 (m-10) REVERT: E 42 LYS cc_start: 0.9132 (mmmm) cc_final: 0.8774 (mmtm) REVERT: E 90 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8401 (t) REVERT: E 138 ILE cc_start: 0.8447 (mm) cc_final: 0.7894 (mm) REVERT: E 165 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7978 (pp) REVERT: E 218 ARG cc_start: 0.8178 (mmp80) cc_final: 0.7603 (tpp-160) REVERT: E 220 GLU cc_start: 0.8161 (mp0) cc_final: 0.7658 (mp0) REVERT: G 12 ARG cc_start: 0.8748 (ptp-170) cc_final: 0.8317 (ptp90) REVERT: G 13 LYS cc_start: 0.8925 (mmtm) cc_final: 0.8620 (mmtm) REVERT: G 47 ASP cc_start: 0.8946 (t0) cc_final: 0.8652 (t0) outliers start: 70 outliers final: 46 residues processed: 236 average time/residue: 0.2201 time to fit residues: 70.6740 Evaluate side-chains 220 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 169 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 175 GLU Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 283 ILE Chi-restraints excluded: chain R residue 299 LEU Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain G residue 25 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 65 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 280 ASN R 314 ASN L 20 HIS ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN B 11 GLN ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 GLN ** 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 = 0.3722 r_free = 0.3722 target = 0.115862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.088171 restraints weight = 16991.166| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.00 r_work: 0.3104 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.7276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9145 Z= 0.293 Angle : 0.646 9.936 12411 Z= 0.328 Chirality : 0.045 0.171 1420 Planarity : 0.004 0.064 1551 Dihedral : 5.805 58.657 1424 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.41 % Allowed : 17.98 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.26), residues: 1110 helix: 1.51 (0.27), residues: 383 sheet: -1.43 (0.29), residues: 271 loop : -1.13 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 21 HIS 0.006 0.001 HIS B 271 PHE 0.023 0.002 PHE R 163 TYR 0.024 0.002 TYR R 199 ARG 0.003 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 183 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 61 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8235 (tt) REVERT: R 97 ASP cc_start: 0.8586 (t0) cc_final: 0.8305 (t70) REVERT: R 205 LEU cc_start: 0.9320 (tp) cc_final: 0.9071 (tt) REVERT: R 212 MET cc_start: 0.8296 (tpp) cc_final: 0.6906 (ttt) REVERT: R 239 GLN cc_start: 0.8513 (tp40) cc_final: 0.8284 (tm-30) REVERT: R 286 TYR cc_start: 0.8440 (t80) cc_final: 0.8220 (t80) REVERT: R 295 ASP cc_start: 0.7956 (p0) cc_final: 0.7264 (p0) REVERT: A 28 GLN cc_start: 0.8881 (tp40) cc_final: 0.8596 (tp40) REVERT: A 315 ASP cc_start: 0.8820 (t0) cc_final: 0.8472 (t0) REVERT: B 203 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8873 (pp) REVERT: B 220 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8463 (pm20) REVERT: B 344 TRP cc_start: 0.8933 (m100) cc_final: 0.8607 (m-10) REVERT: E 90 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8329 (t) REVERT: E 163 LYS cc_start: 0.8510 (tttt) cc_final: 0.8272 (ttpt) REVERT: E 165 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7981 (pp) REVERT: E 202 ARG cc_start: 0.7265 (mtm110) cc_final: 0.6885 (mtm110) REVERT: E 218 ARG cc_start: 0.8198 (mmp80) cc_final: 0.7738 (tpp-160) REVERT: E 220 GLU cc_start: 0.8150 (mp0) cc_final: 0.7526 (mp0) REVERT: G 35 ASP cc_start: 0.8871 (m-30) cc_final: 0.8589 (m-30) REVERT: G 41 GLU cc_start: 0.8842 (pp20) cc_final: 0.8510 (pp20) REVERT: G 47 ASP cc_start: 0.8867 (t0) cc_final: 0.8470 (t0) outliers start: 52 outliers final: 32 residues processed: 218 average time/residue: 0.2155 time to fit residues: 64.2006 Evaluate side-chains 208 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 175 GLU Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 283 ILE Chi-restraints excluded: chain R residue 299 LEU Chi-restraints excluded: chain R residue 305 ILE Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 344 CYS Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain G residue 25 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 12 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 64 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 0.0870 chunk 108 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 201 HIS ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN E 194 ASN ** G 10 GLN ** 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 = 0.3776 r_free = 0.3776 target = 0.119342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.089429 restraints weight = 16825.773| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.91 r_work: 0.3197 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.7115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9145 Z= 0.188 Angle : 0.601 12.058 12411 Z= 0.304 Chirality : 0.044 0.189 1420 Planarity : 0.004 0.056 1551 Dihedral : 5.482 58.666 1424 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.95 % Allowed : 19.75 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.26), residues: 1110 helix: 1.79 (0.27), residues: 379 sheet: -1.22 (0.30), residues: 264 loop : -1.11 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 106 HIS 0.004 0.001 HIS L 25 PHE 0.019 0.001 PHE R 163 TYR 0.014 0.001 TYR R 199 ARG 0.012 0.000 ARG G 12 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 210 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 97 ASP cc_start: 0.8556 (t0) cc_final: 0.8284 (t70) REVERT: R 155 MET cc_start: 0.6007 (tpt) cc_final: 0.5592 (tpp) REVERT: R 205 LEU cc_start: 0.9244 (tp) cc_final: 0.8959 (tt) REVERT: R 211 SER cc_start: 0.8726 (t) cc_final: 0.8470 (m) REVERT: R 212 MET cc_start: 0.8269 (tpp) cc_final: 0.6962 (ttt) REVERT: R 239 GLN cc_start: 0.8373 (tp40) cc_final: 0.8149 (tm-30) REVERT: R 295 ASP cc_start: 0.8078 (p0) cc_final: 0.7435 (p0) REVERT: R 298 MET cc_start: 0.8438 (mmt) cc_final: 0.8032 (tpp) REVERT: L 27 MET cc_start: 0.8384 (mmm) cc_final: 0.8062 (mmm) REVERT: A 28 GLN cc_start: 0.8827 (tp40) cc_final: 0.8060 (tp40) REVERT: A 32 ASP cc_start: 0.8746 (t0) cc_final: 0.8294 (m-30) REVERT: A 315 ASP cc_start: 0.8839 (t0) cc_final: 0.8493 (t70) REVERT: B 106 MET cc_start: 0.9299 (mtp) cc_final: 0.9081 (mtp) REVERT: B 135 GLU cc_start: 0.8730 (mp0) cc_final: 0.8525 (mp0) REVERT: B 193 MET cc_start: 0.8256 (mmt) cc_final: 0.7794 (mmm) REVERT: B 203 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8820 (pp) REVERT: B 216 TRP cc_start: 0.8651 (m100) cc_final: 0.8347 (m100) REVERT: B 334 THR cc_start: 0.9358 (m) cc_final: 0.9108 (p) REVERT: B 344 TRP cc_start: 0.8890 (m100) cc_final: 0.8577 (m-10) REVERT: E 28 PHE cc_start: 0.8916 (t80) cc_final: 0.8625 (t80) REVERT: E 90 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8344 (t) REVERT: E 192 MET cc_start: 0.6287 (ptm) cc_final: 0.5998 (ptm) REVERT: E 202 ARG cc_start: 0.7250 (mtm110) cc_final: 0.6844 (mtm110) REVERT: E 218 ARG cc_start: 0.8301 (mmp80) cc_final: 0.8044 (mmm160) REVERT: E 229 CYS cc_start: 0.8934 (p) cc_final: 0.8552 (p) REVERT: G 12 ARG cc_start: 0.8797 (ptp90) cc_final: 0.8300 (ptp90) REVERT: G 13 LYS cc_start: 0.8939 (mmtm) cc_final: 0.8599 (mmtm) REVERT: G 35 ASP cc_start: 0.8866 (m-30) cc_final: 0.8576 (m-30) REVERT: G 41 GLU cc_start: 0.8687 (pp20) cc_final: 0.8475 (pp20) REVERT: G 47 ASP cc_start: 0.8757 (t0) cc_final: 0.8263 (t0) outliers start: 38 outliers final: 24 residues processed: 233 average time/residue: 0.2209 time to fit residues: 70.4270 Evaluate side-chains 209 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 175 GLU Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 283 ILE Chi-restraints excluded: chain R residue 299 LEU Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain G residue 25 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 22 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 201 HIS ** R 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 290 HIS R 300 HIS A 336 ASN ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 ASN ** G 10 GLN ** 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 = 0.3756 r_free = 0.3756 target = 0.117883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.087997 restraints weight = 17078.915| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.92 r_work: 0.3171 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.7248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9145 Z= 0.224 Angle : 0.628 12.629 12411 Z= 0.316 Chirality : 0.045 0.359 1420 Planarity : 0.004 0.060 1551 Dihedral : 5.367 57.142 1424 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.37 % Allowed : 19.85 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.26), residues: 1110 helix: 1.85 (0.26), residues: 379 sheet: -1.04 (0.30), residues: 259 loop : -1.09 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP L 21 HIS 0.010 0.001 HIS R 300 PHE 0.031 0.001 PHE E 212 TYR 0.014 0.001 TYR R 284 ARG 0.007 0.000 ARG G 12 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 189 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 97 ASP cc_start: 0.8556 (t0) cc_final: 0.8279 (t70) REVERT: R 155 MET cc_start: 0.6055 (tpt) cc_final: 0.5643 (tpp) REVERT: R 205 LEU cc_start: 0.9264 (tp) cc_final: 0.9012 (tt) REVERT: R 212 MET cc_start: 0.8346 (tpp) cc_final: 0.7023 (ttt) REVERT: R 239 GLN cc_start: 0.8383 (tp40) cc_final: 0.8157 (tm-30) REVERT: R 295 ASP cc_start: 0.8013 (p0) cc_final: 0.7644 (p0) REVERT: R 298 MET cc_start: 0.8433 (mmt) cc_final: 0.8072 (tpp) REVERT: L 27 MET cc_start: 0.8313 (mmm) cc_final: 0.7906 (mmm) REVERT: A 28 GLN cc_start: 0.8827 (tp40) cc_final: 0.8013 (tp40) REVERT: A 32 ASP cc_start: 0.8731 (t0) cc_final: 0.8278 (m-30) REVERT: A 315 ASP cc_start: 0.8855 (t0) cc_final: 0.8531 (t70) REVERT: B 193 MET cc_start: 0.8257 (mmt) cc_final: 0.7793 (mmm) REVERT: B 203 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8823 (pp) REVERT: B 216 TRP cc_start: 0.8708 (m100) cc_final: 0.8400 (m100) REVERT: B 220 GLU cc_start: 0.8553 (pm20) cc_final: 0.8224 (pm20) REVERT: B 222 MET cc_start: 0.8262 (ppp) cc_final: 0.7740 (ppp) REVERT: B 334 THR cc_start: 0.9411 (m) cc_final: 0.9066 (p) REVERT: B 344 TRP cc_start: 0.8916 (m100) cc_final: 0.8567 (m-10) REVERT: E 90 THR cc_start: 0.8687 (OUTLIER) cc_final: 0.8334 (t) REVERT: E 160 ARG cc_start: 0.8727 (mtm-85) cc_final: 0.8313 (mpp-170) REVERT: E 202 ARG cc_start: 0.7244 (mtm110) cc_final: 0.6894 (mtm110) REVERT: E 220 GLU cc_start: 0.8179 (mp0) cc_final: 0.7974 (mp0) REVERT: E 223 ASP cc_start: 0.8708 (p0) cc_final: 0.8461 (p0) REVERT: E 229 CYS cc_start: 0.8922 (p) cc_final: 0.8461 (p) REVERT: E 239 PHE cc_start: 0.8872 (m-80) cc_final: 0.8636 (m-80) REVERT: G 12 ARG cc_start: 0.8805 (ptp90) cc_final: 0.8352 (ptp90) REVERT: G 13 LYS cc_start: 0.8946 (mmtm) cc_final: 0.8615 (mmtm) REVERT: G 35 ASP cc_start: 0.8868 (m-30) cc_final: 0.8607 (m-30) REVERT: G 45 LYS cc_start: 0.9159 (mppt) cc_final: 0.8923 (tppt) REVERT: G 47 ASP cc_start: 0.8747 (t0) cc_final: 0.8300 (t0) outliers start: 42 outliers final: 28 residues processed: 215 average time/residue: 0.2015 time to fit residues: 60.2402 Evaluate side-chains 207 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 283 ILE Chi-restraints excluded: chain R residue 299 LEU Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain G residue 25 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 83 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 chunk 43 optimal weight: 0.0770 chunk 67 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 overall best weight: 2.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 149 GLN ** R 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.114498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.083771 restraints weight = 17093.219| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.91 r_work: 0.3098 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.7526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9145 Z= 0.365 Angle : 0.704 12.499 12411 Z= 0.354 Chirality : 0.048 0.375 1420 Planarity : 0.004 0.063 1551 Dihedral : 5.512 54.372 1424 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.74 % Allowed : 21.21 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.25), residues: 1110 helix: 1.67 (0.26), residues: 378 sheet: -0.91 (0.31), residues: 251 loop : -1.15 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP L 21 HIS 0.006 0.001 HIS B 188 PHE 0.024 0.002 PHE E 212 TYR 0.017 0.002 TYR R 286 ARG 0.006 0.001 ARG G 12 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 97 ASP cc_start: 0.8613 (t0) cc_final: 0.8319 (t70) REVERT: R 155 MET cc_start: 0.6104 (tpt) cc_final: 0.5679 (tpp) REVERT: R 205 LEU cc_start: 0.9275 (tp) cc_final: 0.9033 (tt) REVERT: R 239 GLN cc_start: 0.8499 (tp40) cc_final: 0.8230 (tm-30) REVERT: L 27 MET cc_start: 0.8316 (mmm) cc_final: 0.7993 (mmm) REVERT: A 28 GLN cc_start: 0.8847 (tp40) cc_final: 0.8062 (tp40) REVERT: A 32 ASP cc_start: 0.8757 (t0) cc_final: 0.8276 (m-30) REVERT: A 307 TYR cc_start: 0.5591 (m-80) cc_final: 0.5297 (p90) REVERT: A 315 ASP cc_start: 0.8905 (t0) cc_final: 0.8622 (t70) REVERT: B 193 MET cc_start: 0.8399 (mmt) cc_final: 0.7996 (mmm) REVERT: B 203 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8832 (pp) REVERT: B 220 GLU cc_start: 0.8551 (pm20) cc_final: 0.8148 (pm20) REVERT: B 334 THR cc_start: 0.9503 (m) cc_final: 0.9067 (p) REVERT: B 344 TRP cc_start: 0.8927 (m100) cc_final: 0.8566 (m-10) REVERT: E 90 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8396 (t) REVERT: E 160 ARG cc_start: 0.8796 (mtm-85) cc_final: 0.8344 (mpp-170) REVERT: E 220 GLU cc_start: 0.8135 (mp0) cc_final: 0.7929 (mp0) REVERT: E 223 ASP cc_start: 0.8708 (p0) cc_final: 0.8493 (p0) REVERT: E 229 CYS cc_start: 0.8986 (p) cc_final: 0.8697 (p) REVERT: G 12 ARG cc_start: 0.8816 (ptp90) cc_final: 0.8377 (ptp90) REVERT: G 13 LYS cc_start: 0.8923 (mmtm) cc_final: 0.8578 (mmtm) REVERT: G 45 LYS cc_start: 0.9202 (mppt) cc_final: 0.8967 (tppt) REVERT: G 47 ASP cc_start: 0.8854 (t0) cc_final: 0.8399 (t0) outliers start: 36 outliers final: 31 residues processed: 193 average time/residue: 0.2221 time to fit residues: 58.5734 Evaluate side-chains 191 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 175 GLU Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain R residue 194 ILE Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 283 ILE Chi-restraints excluded: chain R residue 299 LEU Chi-restraints excluded: chain R residue 305 ILE Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain G residue 25 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 46 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN ** G 10 GLN ** 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 = 0.3704 r_free = 0.3704 target = 0.114070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.083472 restraints weight = 17251.130| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.89 r_work: 0.3101 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.7553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 9145 Z= 0.353 Angle : 0.969 59.122 12411 Z= 0.547 Chirality : 0.049 0.507 1420 Planarity : 0.004 0.064 1551 Dihedral : 5.522 54.517 1424 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.64 % Allowed : 21.52 % Favored : 74.84 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.25), residues: 1110 helix: 1.69 (0.26), residues: 378 sheet: -0.91 (0.31), residues: 251 loop : -1.18 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP R 106 HIS 0.005 0.001 HIS B 188 PHE 0.025 0.002 PHE E 212 TYR 0.015 0.001 TYR R 199 ARG 0.007 0.001 ARG E 17 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 97 ASP cc_start: 0.8587 (t0) cc_final: 0.8294 (t70) REVERT: R 155 MET cc_start: 0.6010 (tpt) cc_final: 0.5592 (tpp) REVERT: R 205 LEU cc_start: 0.9275 (tp) cc_final: 0.9034 (tt) REVERT: R 239 GLN cc_start: 0.8483 (tp40) cc_final: 0.8221 (tm-30) REVERT: L 27 MET cc_start: 0.8268 (mmm) cc_final: 0.7831 (mmm) REVERT: A 28 GLN cc_start: 0.8851 (tp40) cc_final: 0.8061 (tp40) REVERT: A 32 ASP cc_start: 0.8790 (t0) cc_final: 0.8299 (m-30) REVERT: A 307 TYR cc_start: 0.5617 (m-80) cc_final: 0.5303 (p90) REVERT: A 315 ASP cc_start: 0.8874 (t0) cc_final: 0.8604 (t70) REVERT: B 193 MET cc_start: 0.8398 (mmt) cc_final: 0.8002 (mmm) REVERT: B 203 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8839 (pp) REVERT: B 220 GLU cc_start: 0.8546 (pm20) cc_final: 0.8140 (pm20) REVERT: B 334 THR cc_start: 0.9491 (m) cc_final: 0.9061 (p) REVERT: B 344 TRP cc_start: 0.8931 (m100) cc_final: 0.8576 (m-10) REVERT: E 90 THR cc_start: 0.8752 (OUTLIER) cc_final: 0.8406 (t) REVERT: E 160 ARG cc_start: 0.8776 (mtm-85) cc_final: 0.8330 (mpp-170) REVERT: E 223 ASP cc_start: 0.8707 (p0) cc_final: 0.8500 (p0) REVERT: E 229 CYS cc_start: 0.9007 (p) cc_final: 0.8701 (p) REVERT: G 13 LYS cc_start: 0.8918 (mmtm) cc_final: 0.8551 (mmtm) REVERT: G 45 LYS cc_start: 0.9221 (mppt) cc_final: 0.8978 (tppt) REVERT: G 47 ASP cc_start: 0.8868 (t0) cc_final: 0.8433 (t0) outliers start: 35 outliers final: 32 residues processed: 182 average time/residue: 0.2080 time to fit residues: 52.3031 Evaluate side-chains 192 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 175 GLU Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain R residue 194 ILE Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 227 SER Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 283 ILE Chi-restraints excluded: chain R residue 299 LEU Chi-restraints excluded: chain R residue 305 ILE Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 254 ASP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 87 TRP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain G residue 25 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 14 optimal weight: 0.0970 chunk 24 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 109 optimal weight: 0.0070 chunk 91 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 GLN ** 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 = 0.3704 r_free = 0.3704 target = 0.114085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.083478 restraints weight = 17051.381| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.88 r_work: 0.3100 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.7549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 9145 Z= 0.353 Angle : 0.969 59.122 12411 Z= 0.547 Chirality : 0.049 0.507 1420 Planarity : 0.004 0.065 1551 Dihedral : 5.522 54.517 1424 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.64 % Allowed : 21.52 % Favored : 74.84 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.25), residues: 1110 helix: 1.69 (0.26), residues: 378 sheet: -0.91 (0.31), residues: 251 loop : -1.18 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP R 106 HIS 0.005 0.001 HIS B 188 PHE 0.025 0.002 PHE E 212 TYR 0.015 0.001 TYR R 199 ARG 0.007 0.001 ARG E 17 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4758.95 seconds wall clock time: 83 minutes 33.76 seconds (5013.76 seconds total)