Starting phenix.real_space_refine on Sat Dec 28 20:06:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h0q_34414/12_2024/8h0q_34414.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h0q_34414/12_2024/8h0q_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_34414/12_2024/8h0q_34414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h0q_34414/12_2024/8h0q_34414.map" model { file = "/net/cci-nas-00/data/ceres_data/8h0q_34414/12_2024/8h0q_34414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h0q_34414/12_2024/8h0q_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-5532/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: 5.64, per 1000 atoms: 0.63 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: 2.57 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: 0.93 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: 2.53 Time building geometry restraints manager: 2.94 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: 1.280 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: 0.060 Set scattering table: 0.080 Process input model: 23.120 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.120 ------------------------------------------------------------------------------- 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 : 1.065 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: 0.2880 time to fit residues: 154.8572 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 : 1.154 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 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 : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 61 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8196 (tt) REVERT: R 205 LEU cc_start: 0.9247 (tp) cc_final: 0.9002 (tt) REVERT: R 212 MET cc_start: 0.7484 (tpp) cc_final: 0.6615 (ttt) REVERT: R 286 TYR cc_start: 0.7747 (t80) cc_final: 0.7412 (t80) REVERT: R 295 ASP cc_start: 0.7265 (p0) cc_final: 0.6630 (p0) REVERT: R 309 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8762 (mm) REVERT: L 26 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.6522 (pp) REVERT: A 24 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.7122 (mtm) REVERT: A 26 GLU cc_start: 0.7953 (tp30) cc_final: 0.7643 (mm-30) REVERT: A 28 GLN cc_start: 0.8421 (tp40) cc_final: 0.8212 (tp40) REVERT: A 34 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7785 (mm-40) REVERT: A 249 GLN cc_start: 0.8618 (tp40) cc_final: 0.8400 (tp40) REVERT: B 203 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8737 (pp) REVERT: B 220 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8429 (pm20) REVERT: B 285 LYS cc_start: 0.8471 (ttpt) cc_final: 0.8229 (ttmm) REVERT: B 344 TRP cc_start: 0.8529 (m100) cc_final: 0.8237 (m-10) REVERT: E 2 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7473 (mm-40) REVERT: E 52 SER cc_start: 0.8324 (p) cc_final: 0.8121 (t) REVERT: E 72 ASP cc_start: 0.7286 (t70) cc_final: 0.6852 (p0) REVERT: E 90 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8407 (t) REVERT: E 107 PHE cc_start: 0.8869 (m-80) cc_final: 0.8589 (m-80) REVERT: E 138 ILE cc_start: 0.8456 (mm) cc_final: 0.8242 (mm) REVERT: E 165 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7465 (pp) REVERT: E 202 ARG cc_start: 0.7152 (mtm110) cc_final: 0.6839 (mtm180) REVERT: E 220 GLU cc_start: 0.8138 (mp0) cc_final: 0.7620 (mp0) REVERT: E 223 ASP cc_start: 0.8914 (p0) cc_final: 0.8433 (p0) REVERT: E 228 TYR cc_start: 0.8346 (m-80) cc_final: 0.8129 (m-80) REVERT: G 12 ARG cc_start: 0.8794 (ptp-170) cc_final: 0.8358 (ptp90) REVERT: G 31 LYS cc_start: 0.9147 (tttp) cc_final: 0.8794 (tptm) REVERT: G 35 ASP cc_start: 0.8506 (m-30) cc_final: 0.8045 (m-30) outliers start: 45 outliers final: 24 residues processed: 286 average time/residue: 0.2138 time to fit residues: 83.8088 Evaluate side-chains 243 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 211 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 309 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 55 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 8.9990 chunk 68 optimal weight: 20.0000 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- 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** G 43 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9145 Z= 0.213 Angle : 0.556 6.919 12411 Z= 0.284 Chirality : 0.042 0.169 1420 Planarity : 0.004 0.040 1551 Dihedral : 5.907 53.265 1425 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.41 % Allowed : 15.80 % Favored : 78.79 % 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: -0.46 (0.26), residues: 1110 helix: 1.94 (0.28), residues: 386 sheet: -1.46 (0.30), residues: 255 loop : -1.54 (0.27), residues: 469 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 0.019 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 275 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 223 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 82 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8118 (tt) REVERT: R 205 LEU cc_start: 0.9220 (tp) cc_final: 0.8976 (tt) REVERT: R 286 TYR cc_start: 0.7781 (t80) cc_final: 0.7518 (t80) REVERT: R 293 GLU cc_start: 0.8205 (pm20) cc_final: 0.7909 (pm20) REVERT: R 295 ASP cc_start: 0.7304 (p0) cc_final: 0.6792 (p0) REVERT: L 26 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6807 (pp) REVERT: A 34 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7808 (mm-40) REVERT: A 253 ASN cc_start: 0.9142 (OUTLIER) cc_final: 0.8814 (m110) REVERT: B 203 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8772 (pp) REVERT: B 220 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8403 (pm20) REVERT: B 334 THR cc_start: 0.9143 (m) cc_final: 0.8690 (p) REVERT: B 344 TRP cc_start: 0.8610 (m100) cc_final: 0.8251 (m-10) REVERT: E 72 ASP cc_start: 0.6854 (t70) cc_final: 0.6570 (t70) REVERT: E 82 MET cc_start: 0.7148 (pmm) cc_final: 0.6786 (ptp) REVERT: E 90 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8320 (t) REVERT: E 138 ILE cc_start: 0.8393 (mm) cc_final: 0.7957 (mm) REVERT: E 140 MET cc_start: 0.7474 (pmm) cc_final: 0.7180 (pmm) REVERT: E 165 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7661 (pp) REVERT: E 179 GLN cc_start: 0.7891 (tm-30) cc_final: 0.7618 (tm-30) REVERT: E 223 ASP cc_start: 0.8967 (p0) cc_final: 0.8602 (p0) REVERT: G 12 ARG cc_start: 0.8791 (ptp-170) cc_final: 0.8218 (ptp90) REVERT: G 31 LYS cc_start: 0.9192 (tttp) cc_final: 0.8781 (tptm) REVERT: G 35 ASP cc_start: 0.8543 (m-30) cc_final: 0.8006 (m-30) outliers start: 52 outliers final: 27 residues processed: 256 average time/residue: 0.1957 time to fit residues: 70.9557 Evaluate side-chains 237 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 203 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 ASN Chi-restraints excluded: chain R residue 82 LEU 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 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 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 E residue 194 ASN 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 98 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 chunk 95 optimal weight: 40.0000 chunk 28 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 120 GLN ** R 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 300 HIS R 314 ASN L 20 HIS ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.6136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9145 Z= 0.290 Angle : 0.610 7.637 12411 Z= 0.315 Chirality : 0.044 0.171 1420 Planarity : 0.004 0.035 1551 Dihedral : 5.758 49.196 1425 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 6.24 % Allowed : 16.94 % Favored : 76.82 % 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: -0.27 (0.26), residues: 1110 helix: 1.85 (0.28), residues: 389 sheet: -1.31 (0.30), residues: 264 loop : -1.22 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP L 21 HIS 0.008 0.001 HIS B 147 PHE 0.015 0.002 PHE R 269 TYR 0.018 0.002 TYR R 199 ARG 0.007 0.001 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 282 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 222 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: symmetry clash REVERT: R 205 LEU cc_start: 0.9301 (tp) cc_final: 0.9046 (tt) REVERT: R 293 GLU cc_start: 0.8358 (pm20) cc_final: 0.8019 (pm20) REVERT: A 28 GLN cc_start: 0.8715 (tp40) cc_final: 0.8425 (tp40) REVERT: A 209 GLN cc_start: 0.7162 (mm-40) cc_final: 0.6918 (mm-40) REVERT: A 253 ASN cc_start: 0.9225 (OUTLIER) cc_final: 0.8607 (m110) REVERT: A 297 ARG cc_start: 0.8584 (mtm-85) cc_final: 0.8384 (mtt90) REVERT: B 203 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8750 (pp) REVERT: B 220 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8442 (pm20) REVERT: B 302 TRP cc_start: 0.8903 (m100) cc_final: 0.8485 (m-10) REVERT: B 334 THR cc_start: 0.9255 (m) cc_final: 0.8814 (p) REVERT: B 344 TRP cc_start: 0.8715 (m100) cc_final: 0.8348 (m-10) REVERT: E 2 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7519 (mm-40) REVERT: E 90 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8375 (t) REVERT: E 138 ILE cc_start: 0.8470 (mm) cc_final: 0.8124 (mm) REVERT: E 165 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7817 (pp) REVERT: E 218 ARG cc_start: 0.8107 (mmp80) cc_final: 0.7849 (tpp-160) REVERT: E 220 GLU cc_start: 0.8074 (mp0) cc_final: 0.7595 (mp0) REVERT: E 223 ASP cc_start: 0.8911 (p0) cc_final: 0.8553 (p0) REVERT: G 13 LYS cc_start: 0.8693 (mmtm) cc_final: 0.8424 (mmtm) REVERT: G 31 LYS cc_start: 0.9269 (tttp) cc_final: 0.8906 (tptm) REVERT: G 35 ASP cc_start: 0.8687 (m-30) cc_final: 0.8206 (m-30) REVERT: G 47 ASP cc_start: 0.8818 (t0) cc_final: 0.8576 (t0) outliers start: 60 outliers final: 35 residues processed: 256 average time/residue: 0.2092 time to fit residues: 74.3010 Evaluate side-chains 231 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 76 ASN 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 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 R residue 317 VAL Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 254 ASP 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 93 ASN Chi-restraints excluded: chain B residue 133 THR 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 276 CYS Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain E residue 21 CYS 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 14 LEU 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 88 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 0.0970 chunk 43 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 95 optimal weight: 20.0000 chunk 26 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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** ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.6385 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= 0.213 Angle : 0.586 8.745 12411 Z= 0.296 Chirality : 0.043 0.155 1420 Planarity : 0.004 0.057 1551 Dihedral : 5.546 46.809 1424 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 5.93 % Allowed : 17.78 % 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: -0.12 (0.26), residues: 1110 helix: 1.94 (0.27), residues: 389 sheet: -1.14 (0.31), residues: 256 loop : -1.17 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 21 HIS 0.015 0.001 HIS A 202 PHE 0.032 0.001 PHE R 275 TYR 0.015 0.001 TYR R 199 ARG 0.005 0.000 ARG G 12 *********************** 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 265 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 208 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 205 LEU cc_start: 0.9288 (tp) cc_final: 0.9055 (tt) REVERT: R 212 MET cc_start: 0.7866 (tpp) cc_final: 0.6998 (ttt) REVERT: R 286 TYR cc_start: 0.7917 (t80) cc_final: 0.7594 (t80) REVERT: A 28 GLN cc_start: 0.8711 (tp40) cc_final: 0.7887 (tp40) REVERT: A 32 ASP cc_start: 0.8664 (t0) cc_final: 0.8183 (m-30) REVERT: A 34 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7780 (mm-40) REVERT: A 253 ASN cc_start: 0.9223 (OUTLIER) cc_final: 0.8622 (m110) REVERT: B 203 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8779 (pp) REVERT: B 220 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8440 (pm20) REVERT: B 334 THR cc_start: 0.9206 (m) cc_final: 0.8854 (p) REVERT: B 344 TRP cc_start: 0.8703 (m100) cc_final: 0.8328 (m-10) REVERT: E 72 ASP cc_start: 0.7208 (OUTLIER) cc_final: 0.6796 (p0) REVERT: E 79 PHE cc_start: 0.7747 (m-80) cc_final: 0.7491 (m-80) REVERT: E 90 THR cc_start: 0.8733 (OUTLIER) cc_final: 0.8377 (t) REVERT: E 138 ILE cc_start: 0.8431 (mm) cc_final: 0.8093 (mm) REVERT: G 12 ARG cc_start: 0.8622 (ptp90) cc_final: 0.8300 (ptp90) REVERT: G 31 LYS cc_start: 0.9279 (tttp) cc_final: 0.8880 (tptm) REVERT: G 35 ASP cc_start: 0.8704 (m-30) cc_final: 0.8175 (m-30) REVERT: G 47 ASP cc_start: 0.8801 (t0) cc_final: 0.8547 (t0) outliers start: 57 outliers final: 36 residues processed: 243 average time/residue: 0.1905 time to fit residues: 65.8517 Evaluate side-chains 231 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 190 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 CYS Chi-restraints excluded: chain R residue 76 ASN 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 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 265 THR 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 R residue 317 VAL Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 254 ASP 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 133 THR 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 321 SER Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain G residue 14 LEU 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 35 optimal weight: 2.9990 chunk 95 optimal weight: 30.0000 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 55 optimal weight: 0.0010 chunk 102 optimal weight: 8.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- 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** A 202 HIS ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.6623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9145 Z= 0.251 Angle : 0.598 7.882 12411 Z= 0.307 Chirality : 0.044 0.234 1420 Planarity : 0.003 0.041 1551 Dihedral : 5.421 51.396 1424 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 5.09 % Allowed : 18.09 % Favored : 76.82 % 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: -0.11 (0.26), residues: 1110 helix: 2.00 (0.27), residues: 383 sheet: -1.09 (0.30), residues: 263 loop : -1.20 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 21 HIS 0.006 0.001 HIS A 202 PHE 0.013 0.001 PHE A 194 TYR 0.015 0.001 TYR R 199 ARG 0.004 0.000 ARG G 12 *********************** 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 237 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 188 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 205 LEU cc_start: 0.9298 (tp) cc_final: 0.9070 (tt) REVERT: R 286 TYR cc_start: 0.7964 (t80) cc_final: 0.7643 (t80) REVERT: A 28 GLN cc_start: 0.8752 (tp40) cc_final: 0.7976 (tp40) REVERT: A 32 ASP cc_start: 0.8709 (t0) cc_final: 0.8182 (m-30) REVERT: A 34 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7793 (mm-40) REVERT: A 253 ASN cc_start: 0.9246 (OUTLIER) cc_final: 0.8655 (m110) REVERT: B 8 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7562 (tm-30) REVERT: B 203 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8753 (pp) REVERT: B 220 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8456 (pm20) REVERT: B 302 TRP cc_start: 0.8899 (m100) cc_final: 0.8512 (m-10) REVERT: B 334 THR cc_start: 0.9281 (m) cc_final: 0.8872 (p) REVERT: B 344 TRP cc_start: 0.8733 (m100) cc_final: 0.8353 (m-10) REVERT: E 72 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.6861 (p0) REVERT: E 75 LYS cc_start: 0.8676 (ptpp) cc_final: 0.8150 (ptmm) REVERT: E 90 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8370 (t) REVERT: E 138 ILE cc_start: 0.8492 (mm) cc_final: 0.8182 (mm) REVERT: G 12 ARG cc_start: 0.8694 (ptp90) cc_final: 0.8143 (ptp90) REVERT: G 13 LYS cc_start: 0.8918 (mmtm) cc_final: 0.8705 (mmtt) REVERT: G 15 VAL cc_start: 0.9334 (m) cc_final: 0.9104 (p) REVERT: G 19 LYS cc_start: 0.9147 (mttp) cc_final: 0.8908 (mtmm) REVERT: G 31 LYS cc_start: 0.9308 (tttp) cc_final: 0.8882 (tptm) REVERT: G 35 ASP cc_start: 0.8746 (m-30) cc_final: 0.8195 (m-30) REVERT: G 47 ASP cc_start: 0.8801 (t0) cc_final: 0.8538 (t0) outliers start: 49 outliers final: 37 residues processed: 217 average time/residue: 0.1909 time to fit residues: 59.0670 Evaluate side-chains 224 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 182 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 76 ASN 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 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 265 THR 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 R residue 317 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 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 133 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 228 THR Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 260 LEU 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 66 ARG Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain G residue 14 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 11 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 280 ASN ** B 124 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.6948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9145 Z= 0.285 Angle : 0.627 9.581 12411 Z= 0.320 Chirality : 0.044 0.215 1420 Planarity : 0.003 0.042 1551 Dihedral : 5.382 59.844 1424 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.61 % Allowed : 17.98 % Favored : 76.40 % 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: -0.13 (0.26), residues: 1110 helix: 1.94 (0.27), residues: 383 sheet: -1.14 (0.30), residues: 266 loop : -1.14 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 174 HIS 0.004 0.001 HIS B 147 PHE 0.012 0.001 PHE A 194 TYR 0.016 0.001 TYR R 199 ARG 0.010 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 237 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 183 time to evaluate : 1.073 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: symmetry clash REVERT: R 205 LEU cc_start: 0.9308 (tp) cc_final: 0.9023 (tt) REVERT: R 212 MET cc_start: 0.7803 (tpp) cc_final: 0.6920 (ttp) REVERT: R 286 TYR cc_start: 0.8069 (t80) cc_final: 0.7627 (t80) REVERT: A 28 GLN cc_start: 0.8809 (tp40) cc_final: 0.8041 (tp40) REVERT: A 32 ASP cc_start: 0.8745 (t0) cc_final: 0.8183 (m-30) REVERT: B 203 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8780 (pp) REVERT: B 334 THR cc_start: 0.9317 (m) cc_final: 0.8870 (p) REVERT: B 344 TRP cc_start: 0.8736 (m100) cc_final: 0.8376 (m-10) REVERT: E 72 ASP cc_start: 0.7221 (OUTLIER) cc_final: 0.6852 (p0) REVERT: E 75 LYS cc_start: 0.8673 (ptpp) cc_final: 0.8146 (ptmm) REVERT: E 90 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8387 (t) REVERT: E 138 ILE cc_start: 0.8541 (mm) cc_final: 0.8285 (mm) REVERT: E 223 ASP cc_start: 0.8798 (p0) cc_final: 0.8266 (p0) REVERT: G 12 ARG cc_start: 0.8671 (ptp90) cc_final: 0.8347 (ptp90) REVERT: G 13 LYS cc_start: 0.8949 (mmtm) cc_final: 0.8688 (mmtm) REVERT: G 15 VAL cc_start: 0.9310 (m) cc_final: 0.9098 (p) REVERT: G 35 ASP cc_start: 0.8789 (m-30) cc_final: 0.8463 (m-30) REVERT: G 47 ASP cc_start: 0.8833 (t0) cc_final: 0.8579 (t0) outliers start: 54 outliers final: 42 residues processed: 218 average time/residue: 0.1878 time to fit residues: 58.6482 Evaluate side-chains 226 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 66 CYS 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 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 265 THR 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 R residue 317 VAL Chi-restraints excluded: chain A residue 35 VAL 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 93 ASN Chi-restraints excluded: chain B residue 133 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 228 THR 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 321 SER Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 90 THR 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 63 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 67 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 chunk 83 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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** A 336 ASN ** B 124 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.7093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9145 Z= 0.254 Angle : 0.628 9.234 12411 Z= 0.319 Chirality : 0.045 0.225 1420 Planarity : 0.004 0.061 1551 Dihedral : 5.296 58.369 1424 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 5.51 % Allowed : 18.71 % 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: -0.08 (0.26), residues: 1110 helix: 1.99 (0.27), residues: 383 sheet: -1.03 (0.30), residues: 264 loop : -1.18 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 174 HIS 0.004 0.001 HIS B 147 PHE 0.026 0.001 PHE E 239 TYR 0.016 0.001 TYR R 199 ARG 0.003 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 246 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 193 time to evaluate : 1.067 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: 0.8422 (OUTLIER) cc_final: 0.8214 (tt) REVERT: R 155 MET cc_start: 0.5895 (tpt) cc_final: 0.5501 (tpp) REVERT: R 205 LEU cc_start: 0.9306 (tp) cc_final: 0.9075 (tt) REVERT: R 286 TYR cc_start: 0.8063 (t80) cc_final: 0.7658 (t80) REVERT: A 28 GLN cc_start: 0.8786 (tp40) cc_final: 0.8053 (tp40) REVERT: A 32 ASP cc_start: 0.8754 (t0) cc_final: 0.8171 (m-30) REVERT: B 203 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8781 (pp) REVERT: B 220 GLU cc_start: 0.8487 (pm20) cc_final: 0.8182 (pm20) REVERT: B 222 MET cc_start: 0.7943 (ppp) cc_final: 0.7541 (ppp) REVERT: B 302 TRP cc_start: 0.8897 (m100) cc_final: 0.8545 (m-10) REVERT: B 334 THR cc_start: 0.9309 (m) cc_final: 0.8905 (p) REVERT: B 344 TRP cc_start: 0.8741 (m100) cc_final: 0.8356 (m-10) REVERT: E 72 ASP cc_start: 0.7202 (OUTLIER) cc_final: 0.6761 (p0) REVERT: E 75 LYS cc_start: 0.8654 (ptpp) cc_final: 0.8116 (ptmm) REVERT: E 90 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8370 (t) REVERT: E 138 ILE cc_start: 0.8572 (mm) cc_final: 0.8321 (mm) REVERT: E 223 ASP cc_start: 0.8770 (p0) cc_final: 0.8471 (p0) REVERT: E 229 CYS cc_start: 0.8749 (p) cc_final: 0.8453 (p) REVERT: G 15 VAL cc_start: 0.9318 (m) cc_final: 0.9068 (p) REVERT: G 19 LYS cc_start: 0.9115 (mtmm) cc_final: 0.8874 (mtmm) REVERT: G 35 ASP cc_start: 0.8729 (m-30) cc_final: 0.8489 (m-30) REVERT: G 47 ASP cc_start: 0.8870 (t0) cc_final: 0.8565 (t0) outliers start: 53 outliers final: 41 residues processed: 227 average time/residue: 0.1930 time to fit residues: 62.2552 Evaluate side-chains 227 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 182 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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 66 CYS 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 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 265 THR 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 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 93 ASN Chi-restraints excluded: chain B residue 133 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 228 THR 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 321 SER Chi-restraints excluded: chain E residue 21 CYS Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 90 THR 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 98 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 43 optimal weight: 0.0770 chunk 77 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.5942 ------------------------------------------------------------------------------- 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** A 336 ASN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.7147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9145 Z= 0.250 Angle : 0.649 10.376 12411 Z= 0.330 Chirality : 0.045 0.220 1420 Planarity : 0.004 0.060 1551 Dihedral : 5.236 57.638 1424 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 5.41 % Allowed : 19.44 % Favored : 75.16 % 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: -0.13 (0.26), residues: 1110 helix: 1.98 (0.26), residues: 378 sheet: -1.03 (0.30), residues: 270 loop : -1.22 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 174 HIS 0.003 0.001 HIS B 147 PHE 0.022 0.001 PHE E 239 TYR 0.014 0.001 TYR R 199 ARG 0.004 0.000 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 239 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 187 time to evaluate : 1.038 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 155 MET cc_start: 0.5990 (tpt) cc_final: 0.5601 (tpp) REVERT: R 205 LEU cc_start: 0.9330 (tp) cc_final: 0.9079 (tt) REVERT: R 212 MET cc_start: 0.7769 (tpp) cc_final: 0.6919 (ttp) REVERT: R 286 TYR cc_start: 0.8068 (t80) cc_final: 0.7636 (t80) REVERT: R 298 MET cc_start: 0.8384 (mmt) cc_final: 0.8038 (tpp) REVERT: A 28 GLN cc_start: 0.8798 (tp40) cc_final: 0.8063 (tp40) REVERT: A 32 ASP cc_start: 0.8754 (t0) cc_final: 0.8174 (m-30) REVERT: A 253 ASN cc_start: 0.9241 (OUTLIER) cc_final: 0.8688 (m110) REVERT: B 203 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8732 (pp) REVERT: B 218 VAL cc_start: 0.8363 (t) cc_final: 0.8118 (t) REVERT: B 220 GLU cc_start: 0.8505 (pm20) cc_final: 0.8242 (pm20) REVERT: B 222 MET cc_start: 0.8093 (ppp) cc_final: 0.7702 (ppp) REVERT: B 302 TRP cc_start: 0.8872 (m100) cc_final: 0.8542 (m-10) REVERT: B 334 THR cc_start: 0.9307 (m) cc_final: 0.8886 (p) REVERT: B 344 TRP cc_start: 0.8738 (m100) cc_final: 0.8365 (m-10) REVERT: E 72 ASP cc_start: 0.7174 (OUTLIER) cc_final: 0.6762 (p0) REVERT: E 75 LYS cc_start: 0.8649 (ptpp) cc_final: 0.8125 (ptmm) REVERT: E 90 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8404 (t) REVERT: E 138 ILE cc_start: 0.8591 (mm) cc_final: 0.8376 (mm) REVERT: E 179 GLN cc_start: 0.8259 (tm-30) cc_final: 0.7265 (tm-30) REVERT: E 223 ASP cc_start: 0.8798 (p0) cc_final: 0.8512 (p0) REVERT: E 229 CYS cc_start: 0.8727 (p) cc_final: 0.8486 (p) REVERT: G 35 ASP cc_start: 0.8753 (m-30) cc_final: 0.8526 (m-30) REVERT: G 47 ASP cc_start: 0.8829 (t0) cc_final: 0.8544 (t0) outliers start: 52 outliers final: 41 residues processed: 219 average time/residue: 0.1900 time to fit residues: 59.0198 Evaluate side-chains 218 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 173 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 66 CYS 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 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 265 THR 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 313 THR Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain A residue 35 VAL 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 93 ASN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 276 CYS 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 66 ARG Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain G residue 14 LEU 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: 7.9990 chunk 72 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 100 optimal weight: 0.0980 chunk 87 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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** A 261 ASN A 336 ASN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.7162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9145 Z= 0.207 Angle : 0.662 13.006 12411 Z= 0.336 Chirality : 0.045 0.238 1420 Planarity : 0.004 0.061 1551 Dihedral : 5.123 58.106 1424 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.37 % Allowed : 21.00 % Favored : 74.64 % 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: -0.06 (0.26), residues: 1110 helix: 2.00 (0.26), residues: 379 sheet: -0.94 (0.30), residues: 270 loop : -1.19 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 174 HIS 0.003 0.001 HIS L 25 PHE 0.019 0.001 PHE E 28 TYR 0.012 0.001 TYR R 199 ARG 0.006 0.000 ARG A 37 ********************** 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 231 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 189 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 155 MET cc_start: 0.5971 (tpt) cc_final: 0.5623 (tpp) REVERT: R 205 LEU cc_start: 0.9322 (tp) cc_final: 0.9079 (tt) REVERT: R 212 MET cc_start: 0.7696 (tpp) cc_final: 0.7032 (ttt) REVERT: R 286 TYR cc_start: 0.8077 (t80) cc_final: 0.7669 (t80) REVERT: R 298 MET cc_start: 0.8358 (mmt) cc_final: 0.8022 (mmt) REVERT: A 28 GLN cc_start: 0.8786 (tp40) cc_final: 0.8042 (tp40) REVERT: A 32 ASP cc_start: 0.8739 (t0) cc_final: 0.8165 (m-30) REVERT: A 59 MET cc_start: 0.8721 (ppp) cc_final: 0.8344 (ppp) REVERT: B 106 MET cc_start: 0.9266 (mtp) cc_final: 0.9044 (mtp) REVERT: B 203 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8716 (pp) REVERT: B 218 VAL cc_start: 0.8077 (t) cc_final: 0.7829 (t) REVERT: B 220 GLU cc_start: 0.8652 (pm20) cc_final: 0.8367 (pm20) REVERT: B 222 MET cc_start: 0.8147 (ppp) cc_final: 0.7750 (ppp) REVERT: B 334 THR cc_start: 0.9210 (m) cc_final: 0.8927 (p) REVERT: B 344 TRP cc_start: 0.8686 (m100) cc_final: 0.8345 (m-10) REVERT: E 45 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7970 (pt0) REVERT: E 51 SER cc_start: 0.7877 (m) cc_final: 0.7643 (p) REVERT: E 72 ASP cc_start: 0.7166 (OUTLIER) cc_final: 0.6754 (p0) REVERT: E 75 LYS cc_start: 0.8625 (ptpp) cc_final: 0.8103 (ptmm) REVERT: E 90 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8376 (t) REVERT: E 138 ILE cc_start: 0.8570 (mm) cc_final: 0.8276 (mm) REVERT: E 140 MET cc_start: 0.7715 (pmm) cc_final: 0.7433 (pmm) REVERT: E 179 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7869 (tm-30) REVERT: E 192 MET cc_start: 0.6733 (ptm) cc_final: 0.5740 (ppp) REVERT: E 223 ASP cc_start: 0.8770 (p0) cc_final: 0.8513 (p0) REVERT: G 13 LYS cc_start: 0.8997 (mmtm) cc_final: 0.8655 (mmtm) REVERT: G 35 ASP cc_start: 0.8759 (m-30) cc_final: 0.8532 (m-30) REVERT: G 47 ASP cc_start: 0.8834 (t0) cc_final: 0.8536 (t0) outliers start: 42 outliers final: 32 residues processed: 217 average time/residue: 0.1956 time to fit residues: 60.8175 Evaluate side-chains 212 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 CYS 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 240 SER Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 265 THR 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 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 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 133 THR Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 228 THR 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 61 ASP Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 90 THR 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 80 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 36 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 76 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** A 336 ASN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 HIS ** 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 = 0.3806 r_free = 0.3806 target = 0.120576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.090527 restraints weight = 16786.630| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.90 r_work: 0.3220 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.7131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9145 Z= 0.199 Angle : 0.674 12.589 12411 Z= 0.340 Chirality : 0.045 0.347 1420 Planarity : 0.004 0.059 1551 Dihedral : 5.074 57.819 1424 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.95 % Allowed : 21.62 % Favored : 74.43 % 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: -0.06 (0.26), residues: 1110 helix: 2.00 (0.26), residues: 379 sheet: -0.81 (0.31), residues: 266 loop : -1.28 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 174 HIS 0.003 0.001 HIS R 182 PHE 0.018 0.001 PHE E 28 TYR 0.012 0.001 TYR R 199 ARG 0.017 0.000 ARG G 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2330.84 seconds wall clock time: 43 minutes 29.35 seconds (2609.35 seconds total)