Starting phenix.real_space_refine on Thu Feb 13 12:37:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xqp_38584/02_2025/8xqp_38584.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xqp_38584/02_2025/8xqp_38584.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xqp_38584/02_2025/8xqp_38584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xqp_38584/02_2025/8xqp_38584.map" model { file = "/net/cci-nas-00/data/ceres_data/8xqp_38584/02_2025/8xqp_38584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xqp_38584/02_2025/8xqp_38584.cif" } resolution = 3.29 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= 0.001 sd= 0.023 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 5753 2.51 5 N 1520 2.21 5 O 1656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8987 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1805 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "R" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2317 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 3, 'TRANS': 282} Chain breaks: 2 Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {'CLR': 1, 'GOQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.83, per 1000 atoms: 0.65 Number of scatterers: 8987 At special positions: 0 Unit cell: (88.4, 120.64, 126.88, 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 1656 8.00 N 1520 7.00 C 5753 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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: 2.75 Conformation dependent library (CDL) restraints added in 1.2 seconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 14 sheets defined 40.6% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 21 through 45 Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 211 through 218 removed outlier: 3.561A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLY A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.019A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.226A pdb=" N THR A 279 " --> pdb=" O GLN A 275 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.756A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'R' and resid 3 through 37 removed outlier: 3.588A pdb=" N LYS R 37 " --> pdb=" O ILE R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 71 Processing helix chain 'R' and resid 72 through 77 removed outlier: 3.788A pdb=" N PHE R 76 " --> pdb=" O PHE R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 112 Processing helix chain 'R' and resid 116 through 125 Processing helix chain 'R' and resid 125 through 162 removed outlier: 4.244A pdb=" N SER R 138 " --> pdb=" O LEU R 134 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N VAL R 139 " --> pdb=" O LEU R 135 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE R 140 " --> pdb=" O VAL R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 215 Proline residue: R 190 - end of helix removed outlier: 3.671A pdb=" N LEU R 193 " --> pdb=" O ILE R 189 " (cutoff:3.500A) Processing helix chain 'R' and resid 222 through 228 Processing helix chain 'R' and resid 232 through 253 removed outlier: 3.514A pdb=" N LEU R 239 " --> pdb=" O THR R 235 " (cutoff:3.500A) Processing helix chain 'R' and resid 260 through 270 Processing helix chain 'R' and resid 270 through 275 Processing helix chain 'R' and resid 275 through 284 removed outlier: 3.598A pdb=" N VAL R 279 " --> pdb=" O CYS R 275 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 299 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.881A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.633A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.194A pdb=" N VAL A 49 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N PHE A 199 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU A 51 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N CYS A 220 " --> pdb=" O LYS A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.450A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.760A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.212A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.657A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.167A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.643A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.525A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 6 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 5.905A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 58 through 60 removed outlier: 5.905A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.548A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 498 hydrogen bonds defined for protein. 1419 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: 3.23 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1436 1.28 - 1.41: 2354 1.41 - 1.55: 5289 1.55 - 1.68: 12 1.68 - 1.81: 86 Bond restraints: 9177 Sorted by residual: bond pdb=" C CYS R 275 " pdb=" O CYS R 275 " ideal model delta sigma weight residual 1.236 1.141 0.095 1.15e-02 7.56e+03 6.79e+01 bond pdb=" C TYR R 272 " pdb=" O TYR R 272 " ideal model delta sigma weight residual 1.244 1.176 0.067 9.80e-03 1.04e+04 4.73e+01 bond pdb=" N MET R 270 " pdb=" CA MET R 270 " ideal model delta sigma weight residual 1.456 1.383 0.074 1.31e-02 5.83e+03 3.17e+01 bond pdb=" C TYR R 272 " pdb=" N PRO R 273 " ideal model delta sigma weight residual 1.335 1.272 0.063 1.30e-02 5.92e+03 2.35e+01 bond pdb=" C MET R 270 " pdb=" O MET R 270 " ideal model delta sigma weight residual 1.236 1.175 0.061 1.31e-02 5.83e+03 2.14e+01 ... (remaining 9172 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 12279 2.74 - 5.47: 125 5.47 - 8.21: 10 8.21 - 10.94: 2 10.94 - 13.68: 5 Bond angle restraints: 12421 Sorted by residual: angle pdb=" N CYS R 278 " pdb=" CA CYS R 278 " pdb=" C CYS R 278 " ideal model delta sigma weight residual 112.23 100.90 11.33 1.26e+00 6.30e-01 8.09e+01 angle pdb=" N HIS R 276 " pdb=" CA HIS R 276 " pdb=" C HIS R 276 " ideal model delta sigma weight residual 110.80 124.48 -13.68 2.13e+00 2.20e-01 4.12e+01 angle pdb=" CA CYS R 278 " pdb=" C CYS R 278 " pdb=" O CYS R 278 " ideal model delta sigma weight residual 119.79 125.20 -5.41 1.18e+00 7.18e-01 2.10e+01 angle pdb=" CA CYS R 278 " pdb=" C CYS R 278 " pdb=" N VAL R 279 " ideal model delta sigma weight residual 117.82 111.58 6.24 1.42e+00 4.96e-01 1.93e+01 angle pdb=" N SER R 277 " pdb=" CA SER R 277 " pdb=" C SER R 277 " ideal model delta sigma weight residual 113.17 108.34 4.83 1.26e+00 6.30e-01 1.47e+01 ... (remaining 12416 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 4678 17.20 - 34.39: 579 34.39 - 51.59: 160 51.59 - 68.79: 36 68.79 - 85.99: 10 Dihedral angle restraints: 5463 sinusoidal: 2177 harmonic: 3286 Sorted by residual: dihedral pdb=" N HIS R 276 " pdb=" C HIS R 276 " pdb=" CA HIS R 276 " pdb=" CB HIS R 276 " ideal model delta harmonic sigma weight residual 122.80 142.33 -19.53 0 2.50e+00 1.60e-01 6.10e+01 dihedral pdb=" C HIS R 276 " pdb=" N HIS R 276 " pdb=" CA HIS R 276 " pdb=" CB HIS R 276 " ideal model delta harmonic sigma weight residual -122.60 -141.88 19.28 0 2.50e+00 1.60e-01 5.95e+01 dihedral pdb=" CD ARG S 98 " pdb=" NE ARG S 98 " pdb=" CZ ARG S 98 " pdb=" NH1 ARG S 98 " ideal model delta sinusoidal sigma weight residual 0.00 57.40 -57.40 1 1.00e+01 1.00e-02 4.43e+01 ... (remaining 5460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.200: 1411 0.200 - 0.401: 3 0.401 - 0.601: 1 0.601 - 0.802: 0 0.802 - 1.002: 1 Chirality restraints: 1416 Sorted by residual: chirality pdb=" CA HIS R 276 " pdb=" N HIS R 276 " pdb=" C HIS R 276 " pdb=" CB HIS R 276 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.51e+01 chirality pdb=" CA TYR R 272 " pdb=" N TYR R 272 " pdb=" C TYR R 272 " pdb=" CB TYR R 272 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.02e+00 chirality pdb=" CB VAL A 49 " pdb=" CA VAL A 49 " pdb=" CG1 VAL A 49 " pdb=" CG2 VAL A 49 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 1413 not shown) Planarity restraints: 1547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG S 98 " 0.937 9.50e-02 1.11e+02 4.20e-01 1.07e+02 pdb=" NE ARG S 98 " -0.055 2.00e-02 2.50e+03 pdb=" CZ ARG S 98 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG S 98 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG S 98 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR R 272 " -0.069 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO R 273 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO R 273 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO R 273 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE R 72 " -0.053 5.00e-02 4.00e+02 8.02e-02 1.03e+01 pdb=" N PRO R 73 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO R 73 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO R 73 " -0.044 5.00e-02 4.00e+02 ... (remaining 1544 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 437 2.72 - 3.26: 9224 3.26 - 3.81: 15660 3.81 - 4.35: 18769 4.35 - 4.90: 31481 Nonbonded interactions: 75571 Sorted by model distance: nonbonded pdb=" OG SER S 149 " pdb=" O LYS S 151 " model vdw 2.173 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.180 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.195 3.040 nonbonded pdb=" O ILE S 126 " pdb=" OG1 THR S 226 " model vdw 2.201 3.040 nonbonded pdb=" O TYR S 102 " pdb=" OG SER S 105 " model vdw 2.234 3.040 ... (remaining 75566 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.820 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 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 : 0.004 0.095 9177 Z= 0.303 Angle : 0.709 13.677 12421 Z= 0.389 Chirality : 0.054 1.002 1416 Planarity : 0.012 0.420 1547 Dihedral : 16.653 85.987 3331 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.30 % Allowed : 30.28 % Favored : 69.41 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.26), residues: 1118 helix: 2.16 (0.26), residues: 422 sheet: -0.79 (0.31), residues: 287 loop : -0.76 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP R 66 HIS 0.012 0.001 HIS R 276 PHE 0.031 0.002 PHE A 189 TYR 0.022 0.002 TYR S 102 ARG 0.007 0.001 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 276 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: A 28 VAL cc_start: 0.8424 (t) cc_final: 0.8193 (t) REVERT: A 192 LYS cc_start: 0.8170 (mttp) cc_final: 0.7957 (mmtp) REVERT: A 232 MET cc_start: 0.6453 (mmm) cc_final: 0.6137 (mmm) REVERT: A 317 LYS cc_start: 0.7821 (ptmm) cc_final: 0.7589 (ptmm) REVERT: B 196 THR cc_start: 0.7927 (p) cc_final: 0.7650 (p) REVERT: B 209 LYS cc_start: 0.8346 (mttm) cc_final: 0.8018 (mttm) REVERT: B 214 ARG cc_start: 0.7127 (mtp85) cc_final: 0.6927 (mtp85) REVERT: R 98 TRP cc_start: 0.8446 (m100) cc_final: 0.7846 (m100) REVERT: R 125 ARG cc_start: 0.7700 (mtt180) cc_final: 0.7494 (mtt180) REVERT: R 273 PRO cc_start: 0.8493 (OUTLIER) cc_final: 0.8177 (Cg_endo) REVERT: S 73 ASP cc_start: 0.7167 (t0) cc_final: 0.6839 (t70) REVERT: S 219 GLN cc_start: 0.8058 (pp30) cc_final: 0.7824 (pp30) outliers start: 3 outliers final: 2 residues processed: 278 average time/residue: 0.2746 time to fit residues: 98.8602 Evaluate side-chains 278 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 275 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 270 MET Chi-restraints excluded: chain R residue 272 TYR Chi-restraints excluded: chain R residue 273 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 46 optimal weight: 0.0270 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 301 ASN B 32 GLN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.157793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.133730 restraints weight = 14239.662| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.62 r_work: 0.3574 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9177 Z= 0.232 Angle : 0.601 10.888 12421 Z= 0.316 Chirality : 0.043 0.221 1416 Planarity : 0.005 0.076 1547 Dihedral : 5.902 87.881 1298 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.86 % Allowed : 24.90 % Favored : 71.24 % 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: 0.56 (0.26), residues: 1118 helix: 2.27 (0.25), residues: 429 sheet: -0.80 (0.30), residues: 287 loop : -0.76 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.005 0.001 HIS B 54 PHE 0.018 0.002 PHE R 236 TYR 0.032 0.002 TYR S 223 ARG 0.005 0.001 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 267 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 28 VAL cc_start: 0.8249 (t) cc_final: 0.8024 (t) REVERT: A 192 LYS cc_start: 0.8261 (mttp) cc_final: 0.8011 (mmtp) REVERT: A 201 VAL cc_start: 0.7604 (OUTLIER) cc_final: 0.7381 (t) REVERT: A 219 THR cc_start: 0.8339 (p) cc_final: 0.8014 (t) REVERT: A 232 MET cc_start: 0.6551 (mmm) cc_final: 0.6298 (mmm) REVERT: A 317 LYS cc_start: 0.7745 (ptmm) cc_final: 0.7443 (ptmm) REVERT: B 15 LYS cc_start: 0.8970 (mtpt) cc_final: 0.8681 (mtpt) REVERT: B 68 ARG cc_start: 0.5904 (ttp-170) cc_final: 0.5338 (ttp-170) REVERT: B 129 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.6629 (mmp80) REVERT: B 196 THR cc_start: 0.7937 (p) cc_final: 0.7687 (p) REVERT: B 209 LYS cc_start: 0.8417 (mttm) cc_final: 0.8079 (mttm) REVERT: B 210 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7843 (tp) REVERT: B 214 ARG cc_start: 0.7693 (mtp85) cc_final: 0.6483 (mtp85) REVERT: B 217 MET cc_start: 0.6504 (ppp) cc_final: 0.5862 (ppp) REVERT: C 22 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6673 (mp0) REVERT: C 27 ARG cc_start: 0.7059 (mtm-85) cc_final: 0.6654 (mmt90) REVERT: R 65 SER cc_start: 0.9023 (OUTLIER) cc_final: 0.8805 (m) REVERT: R 125 ARG cc_start: 0.7870 (mtt180) cc_final: 0.7382 (mtt180) REVERT: R 147 LEU cc_start: 0.6617 (pp) cc_final: 0.6100 (tt) REVERT: R 205 MET cc_start: 0.8295 (tpp) cc_final: 0.7763 (tpp) REVERT: S 157 ASN cc_start: 0.8263 (p0) cc_final: 0.8016 (p0) outliers start: 38 outliers final: 16 residues processed: 288 average time/residue: 0.2619 time to fit residues: 98.0351 Evaluate side-chains 280 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 259 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 65 SER Chi-restraints excluded: chain R residue 272 TYR Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 160 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 85 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 87 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 331 ASN B 220 GLN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.157463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.132860 restraints weight = 14409.733| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.65 r_work: 0.3565 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9177 Z= 0.242 Angle : 0.583 8.808 12421 Z= 0.306 Chirality : 0.042 0.233 1416 Planarity : 0.005 0.064 1547 Dihedral : 5.763 86.920 1292 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.67 % Allowed : 25.20 % Favored : 70.12 % 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: 0.51 (0.26), residues: 1118 helix: 2.27 (0.25), residues: 430 sheet: -0.97 (0.30), residues: 288 loop : -0.71 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.003 0.001 HIS B 54 PHE 0.020 0.002 PHE A 196 TYR 0.034 0.002 TYR S 223 ARG 0.006 0.001 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 268 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: A 28 VAL cc_start: 0.8276 (t) cc_final: 0.8062 (t) REVERT: A 29 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7110 (mm-30) REVERT: A 61 LYS cc_start: 0.6668 (mtmt) cc_final: 0.6326 (ttpp) REVERT: A 192 LYS cc_start: 0.8192 (mttp) cc_final: 0.7917 (mmtp) REVERT: A 219 THR cc_start: 0.8332 (p) cc_final: 0.7965 (t) REVERT: A 232 MET cc_start: 0.6645 (mmm) cc_final: 0.6297 (mmm) REVERT: A 242 ARG cc_start: 0.7700 (mtt180) cc_final: 0.7118 (mtt-85) REVERT: A 245 GLU cc_start: 0.7999 (tp30) cc_final: 0.7691 (tp30) REVERT: A 317 LYS cc_start: 0.7756 (ptmm) cc_final: 0.7305 (ttpp) REVERT: A 346 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7407 (tm-30) REVERT: B 15 LYS cc_start: 0.8986 (mtpt) cc_final: 0.8671 (mtpt) REVERT: B 68 ARG cc_start: 0.5850 (ttp-170) cc_final: 0.5440 (ttt-90) REVERT: B 196 THR cc_start: 0.7870 (p) cc_final: 0.7576 (p) REVERT: B 197 ARG cc_start: 0.7269 (mtp85) cc_final: 0.6986 (mtp-110) REVERT: B 209 LYS cc_start: 0.8539 (mttm) cc_final: 0.8336 (mttp) REVERT: B 210 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7901 (tp) REVERT: B 214 ARG cc_start: 0.7256 (mtp85) cc_final: 0.7039 (mtp85) REVERT: B 314 ARG cc_start: 0.7688 (mtp180) cc_final: 0.7261 (ttm170) REVERT: C 21 MET cc_start: 0.7291 (mmm) cc_final: 0.6982 (mmm) REVERT: C 22 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6614 (mp0) REVERT: C 27 ARG cc_start: 0.7143 (mtm-85) cc_final: 0.6432 (mmt90) REVERT: R 99 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8230 (tp) REVERT: R 125 ARG cc_start: 0.7871 (mtt180) cc_final: 0.7425 (mtt180) REVERT: R 147 LEU cc_start: 0.6660 (pp) cc_final: 0.6164 (tt) REVERT: R 205 MET cc_start: 0.8292 (tpp) cc_final: 0.7851 (tpp) REVERT: R 268 MET cc_start: 0.7736 (tmm) cc_final: 0.7342 (tmm) REVERT: S 146 SER cc_start: 0.7789 (p) cc_final: 0.7578 (t) REVERT: S 232 LYS cc_start: 0.7889 (tptm) cc_final: 0.7466 (tptm) outliers start: 46 outliers final: 27 residues processed: 296 average time/residue: 0.2682 time to fit residues: 103.2607 Evaluate side-chains 300 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 270 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 272 TYR Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 26 optimal weight: 0.7980 chunk 93 optimal weight: 0.0470 chunk 54 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 15 optimal weight: 0.2980 chunk 1 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 104 optimal weight: 0.7980 chunk 50 optimal weight: 0.0770 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.160312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.136453 restraints weight = 14287.464| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.63 r_work: 0.3595 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9177 Z= 0.164 Angle : 0.543 7.756 12421 Z= 0.284 Chirality : 0.041 0.211 1416 Planarity : 0.004 0.065 1547 Dihedral : 5.549 87.098 1292 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.07 % Allowed : 26.02 % Favored : 69.92 % 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: 0.64 (0.26), residues: 1118 helix: 2.38 (0.25), residues: 430 sheet: -0.87 (0.30), residues: 290 loop : -0.67 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 169 HIS 0.002 0.001 HIS B 54 PHE 0.017 0.001 PHE A 196 TYR 0.031 0.001 TYR S 223 ARG 0.005 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 268 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 VAL cc_start: 0.8256 (t) cc_final: 0.8030 (t) REVERT: A 29 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7120 (mm-30) REVERT: A 61 LYS cc_start: 0.6630 (mtmt) cc_final: 0.6410 (mtmt) REVERT: A 192 LYS cc_start: 0.8221 (mttp) cc_final: 0.7934 (mmtp) REVERT: A 219 THR cc_start: 0.8304 (p) cc_final: 0.7922 (t) REVERT: A 232 MET cc_start: 0.6598 (mmm) cc_final: 0.6249 (mmm) REVERT: A 242 ARG cc_start: 0.7688 (mtt180) cc_final: 0.7142 (mtt-85) REVERT: A 245 GLU cc_start: 0.7965 (tp30) cc_final: 0.7660 (tp30) REVERT: A 274 PHE cc_start: 0.7006 (t80) cc_final: 0.6591 (t80) REVERT: A 317 LYS cc_start: 0.7746 (ptmm) cc_final: 0.7331 (ttpp) REVERT: B 15 LYS cc_start: 0.8993 (mtpt) cc_final: 0.8671 (mtpt) REVERT: B 68 ARG cc_start: 0.5824 (ttp-170) cc_final: 0.5415 (ttt-90) REVERT: B 127 LYS cc_start: 0.8332 (mmmm) cc_final: 0.7889 (mttm) REVERT: B 159 THR cc_start: 0.7719 (m) cc_final: 0.7353 (p) REVERT: B 196 THR cc_start: 0.7724 (p) cc_final: 0.7476 (p) REVERT: B 197 ARG cc_start: 0.7164 (mtp85) cc_final: 0.6952 (mtp-110) REVERT: B 210 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7672 (tp) REVERT: B 214 ARG cc_start: 0.7299 (mtp85) cc_final: 0.7013 (mtp85) REVERT: C 21 MET cc_start: 0.7175 (mmm) cc_final: 0.6808 (mmm) REVERT: C 27 ARG cc_start: 0.7089 (mtm-85) cc_final: 0.6648 (mmt90) REVERT: R 37 LYS cc_start: 0.7632 (pttp) cc_final: 0.7276 (pptt) REVERT: R 99 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8193 (tp) REVERT: R 125 ARG cc_start: 0.7840 (mtt180) cc_final: 0.7381 (mtt180) REVERT: R 140 PHE cc_start: 0.7649 (m-80) cc_final: 0.7259 (t80) REVERT: R 147 LEU cc_start: 0.6782 (pp) cc_final: 0.6230 (tt) REVERT: R 205 MET cc_start: 0.8197 (tpp) cc_final: 0.7583 (tpp) REVERT: R 237 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.7590 (t80) REVERT: R 268 MET cc_start: 0.7573 (tmm) cc_final: 0.7303 (tmm) REVERT: S 222 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6806 (mm-30) outliers start: 40 outliers final: 27 residues processed: 290 average time/residue: 0.2544 time to fit residues: 95.6370 Evaluate side-chains 295 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 265 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 272 TYR Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 22 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 57 optimal weight: 0.0570 chunk 69 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 293 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.157933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.133639 restraints weight = 14327.748| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.65 r_work: 0.3575 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9177 Z= 0.212 Angle : 0.557 8.315 12421 Z= 0.291 Chirality : 0.041 0.213 1416 Planarity : 0.004 0.063 1547 Dihedral : 5.557 87.419 1292 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.98 % Allowed : 26.12 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 1118 helix: 2.41 (0.25), residues: 431 sheet: -0.90 (0.29), residues: 290 loop : -0.63 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS B 266 PHE 0.015 0.001 PHE R 106 TYR 0.032 0.002 TYR S 223 ARG 0.007 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 267 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 VAL cc_start: 0.8281 (t) cc_final: 0.8040 (t) REVERT: A 29 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7095 (mm-30) REVERT: A 192 LYS cc_start: 0.8164 (mttp) cc_final: 0.7888 (mmtp) REVERT: A 219 THR cc_start: 0.8334 (p) cc_final: 0.7974 (t) REVERT: A 232 MET cc_start: 0.6700 (mmm) cc_final: 0.6315 (mmm) REVERT: A 242 ARG cc_start: 0.7735 (mtt180) cc_final: 0.7517 (mtt180) REVERT: A 245 GLU cc_start: 0.7993 (tp30) cc_final: 0.7680 (tp30) REVERT: A 274 PHE cc_start: 0.7053 (t80) cc_final: 0.6652 (t80) REVERT: A 305 ASN cc_start: 0.7692 (m110) cc_final: 0.7322 (m110) REVERT: A 317 LYS cc_start: 0.7735 (ptmm) cc_final: 0.7319 (ttpp) REVERT: B 15 LYS cc_start: 0.8985 (mtpt) cc_final: 0.8647 (mtpt) REVERT: B 68 ARG cc_start: 0.5804 (ttp-170) cc_final: 0.5434 (ttt-90) REVERT: B 127 LYS cc_start: 0.8330 (mmmm) cc_final: 0.7896 (mttm) REVERT: B 196 THR cc_start: 0.7768 (p) cc_final: 0.7471 (p) REVERT: B 197 ARG cc_start: 0.7240 (mtp85) cc_final: 0.7011 (mtp85) REVERT: B 210 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7760 (tp) REVERT: B 214 ARG cc_start: 0.7346 (mtp85) cc_final: 0.7006 (mtp85) REVERT: B 220 GLN cc_start: 0.8137 (mt0) cc_final: 0.7805 (mt0) REVERT: B 284 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.8024 (tp) REVERT: B 314 ARG cc_start: 0.7584 (mtp180) cc_final: 0.7175 (ttm-80) REVERT: C 22 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6758 (mp0) REVERT: R 71 PHE cc_start: 0.6342 (m-80) cc_final: 0.6086 (m-10) REVERT: R 99 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8219 (tp) REVERT: R 125 ARG cc_start: 0.7896 (mtt180) cc_final: 0.7344 (mtt180) REVERT: R 140 PHE cc_start: 0.7672 (OUTLIER) cc_final: 0.7268 (t80) REVERT: R 147 LEU cc_start: 0.6807 (pp) cc_final: 0.6276 (tt) REVERT: R 205 MET cc_start: 0.8239 (tpp) cc_final: 0.7592 (tpp) REVERT: R 268 MET cc_start: 0.7581 (tmm) cc_final: 0.7333 (tmm) REVERT: S 222 GLU cc_start: 0.7342 (mm-30) cc_final: 0.6842 (mm-30) outliers start: 49 outliers final: 33 residues processed: 294 average time/residue: 0.2711 time to fit residues: 102.7087 Evaluate side-chains 310 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 272 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 3 optimal weight: 0.0000 chunk 42 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 15 optimal weight: 0.0040 chunk 56 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.160051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.135657 restraints weight = 14339.204| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.69 r_work: 0.3577 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9177 Z= 0.184 Angle : 0.545 7.149 12421 Z= 0.286 Chirality : 0.041 0.201 1416 Planarity : 0.004 0.064 1547 Dihedral : 5.309 87.364 1290 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.57 % Allowed : 26.52 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.26), residues: 1118 helix: 2.51 (0.25), residues: 425 sheet: -0.88 (0.29), residues: 290 loop : -0.54 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS B 266 PHE 0.019 0.001 PHE R 76 TYR 0.032 0.001 TYR S 223 ARG 0.007 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 267 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 VAL cc_start: 0.8270 (t) cc_final: 0.8043 (t) REVERT: A 29 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7081 (mm-30) REVERT: A 48 THR cc_start: 0.8103 (t) cc_final: 0.7845 (t) REVERT: A 189 PHE cc_start: 0.8105 (p90) cc_final: 0.7895 (p90) REVERT: A 192 LYS cc_start: 0.8164 (mttp) cc_final: 0.7888 (mmtp) REVERT: A 219 THR cc_start: 0.8305 (p) cc_final: 0.7928 (t) REVERT: A 232 MET cc_start: 0.6768 (mmm) cc_final: 0.6349 (mmm) REVERT: A 242 ARG cc_start: 0.7726 (mtt180) cc_final: 0.7473 (mtt180) REVERT: A 245 GLU cc_start: 0.8010 (tp30) cc_final: 0.7685 (tp30) REVERT: A 274 PHE cc_start: 0.7044 (t80) cc_final: 0.6664 (t80) REVERT: A 305 ASN cc_start: 0.7766 (m110) cc_final: 0.7557 (m110) REVERT: A 317 LYS cc_start: 0.7745 (ptmm) cc_final: 0.7323 (ttpp) REVERT: A 346 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7413 (mm-30) REVERT: B 15 LYS cc_start: 0.8981 (mtpt) cc_final: 0.8598 (mtpt) REVERT: B 68 ARG cc_start: 0.5816 (ttp-170) cc_final: 0.5437 (ttt-90) REVERT: B 127 LYS cc_start: 0.8318 (mmmm) cc_final: 0.7835 (mttm) REVERT: B 196 THR cc_start: 0.7715 (p) cc_final: 0.7437 (p) REVERT: B 197 ARG cc_start: 0.7250 (mtp85) cc_final: 0.7017 (mtp85) REVERT: B 210 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7744 (tp) REVERT: B 214 ARG cc_start: 0.7360 (mtp85) cc_final: 0.7041 (mtp85) REVERT: B 258 ASP cc_start: 0.6432 (t0) cc_final: 0.6175 (t0) REVERT: B 266 HIS cc_start: 0.7512 (t70) cc_final: 0.7290 (t70) REVERT: B 314 ARG cc_start: 0.7536 (mtp180) cc_final: 0.7229 (ttm170) REVERT: C 22 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6691 (mp0) REVERT: C 27 ARG cc_start: 0.7081 (mtm-85) cc_final: 0.6644 (mmt90) REVERT: R 71 PHE cc_start: 0.6181 (m-80) cc_final: 0.5942 (m-10) REVERT: R 99 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8194 (tp) REVERT: R 108 PHE cc_start: 0.8453 (t80) cc_final: 0.8230 (t80) REVERT: R 125 ARG cc_start: 0.7895 (mtt180) cc_final: 0.7388 (mtt180) REVERT: R 140 PHE cc_start: 0.7678 (OUTLIER) cc_final: 0.7276 (t80) REVERT: R 143 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6599 (tt) REVERT: R 147 LEU cc_start: 0.6788 (pp) cc_final: 0.6263 (tt) REVERT: R 205 MET cc_start: 0.8208 (tpp) cc_final: 0.7576 (tpp) REVERT: R 268 MET cc_start: 0.7608 (tmm) cc_final: 0.7325 (tmm) REVERT: S 222 GLU cc_start: 0.7269 (mm-30) cc_final: 0.6774 (mm-30) outliers start: 45 outliers final: 31 residues processed: 294 average time/residue: 0.2705 time to fit residues: 103.4004 Evaluate side-chains 302 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 266 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.157755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.133832 restraints weight = 14517.759| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.62 r_work: 0.3555 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9177 Z= 0.311 Angle : 0.606 8.591 12421 Z= 0.316 Chirality : 0.043 0.218 1416 Planarity : 0.004 0.064 1547 Dihedral : 5.566 88.738 1290 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 5.79 % Allowed : 26.32 % Favored : 67.89 % 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: 0.66 (0.26), residues: 1118 helix: 2.43 (0.25), residues: 426 sheet: -0.96 (0.29), residues: 290 loop : -0.58 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 169 HIS 0.004 0.001 HIS B 266 PHE 0.020 0.002 PHE A 196 TYR 0.035 0.002 TYR S 223 ARG 0.007 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 271 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 THR cc_start: 0.8154 (t) cc_final: 0.7932 (t) REVERT: A 50 LYS cc_start: 0.7909 (ttmm) cc_final: 0.7530 (mtpp) REVERT: A 192 LYS cc_start: 0.8139 (mttp) cc_final: 0.7865 (mmtp) REVERT: A 219 THR cc_start: 0.8368 (p) cc_final: 0.8004 (t) REVERT: A 232 MET cc_start: 0.6749 (mmm) cc_final: 0.6354 (mmm) REVERT: A 242 ARG cc_start: 0.7848 (mtt180) cc_final: 0.7514 (mtt180) REVERT: A 245 GLU cc_start: 0.8019 (tp30) cc_final: 0.7675 (tp30) REVERT: A 274 PHE cc_start: 0.7067 (t80) cc_final: 0.6693 (t80) REVERT: A 305 ASN cc_start: 0.7779 (m110) cc_final: 0.7356 (m110) REVERT: A 317 LYS cc_start: 0.7730 (ptmm) cc_final: 0.7263 (ptmm) REVERT: A 346 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7397 (tm-30) REVERT: B 15 LYS cc_start: 0.8962 (mtpt) cc_final: 0.8650 (mtpt) REVERT: B 55 LEU cc_start: 0.8472 (mm) cc_final: 0.8162 (mp) REVERT: B 68 ARG cc_start: 0.5845 (ttp-170) cc_final: 0.5370 (ttp80) REVERT: B 153 ASP cc_start: 0.6753 (m-30) cc_final: 0.6404 (m-30) REVERT: B 196 THR cc_start: 0.7836 (p) cc_final: 0.7534 (p) REVERT: B 197 ARG cc_start: 0.7319 (mtp85) cc_final: 0.7076 (mtp85) REVERT: B 214 ARG cc_start: 0.7429 (mtp85) cc_final: 0.7113 (mtp85) REVERT: B 258 ASP cc_start: 0.6415 (t0) cc_final: 0.6170 (t0) REVERT: B 284 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8053 (tp) REVERT: C 21 MET cc_start: 0.7352 (mmm) cc_final: 0.6982 (mmm) REVERT: C 22 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6631 (mp0) REVERT: R 37 LYS cc_start: 0.7597 (pttp) cc_final: 0.7289 (pptt) REVERT: R 62 ILE cc_start: 0.8466 (tp) cc_final: 0.7512 (pt) REVERT: R 125 ARG cc_start: 0.7889 (mtt180) cc_final: 0.7415 (mtt180) REVERT: R 140 PHE cc_start: 0.7741 (OUTLIER) cc_final: 0.7288 (t80) REVERT: R 143 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.6536 (tt) REVERT: R 147 LEU cc_start: 0.6809 (pp) cc_final: 0.6313 (tt) REVERT: R 205 MET cc_start: 0.8267 (tpp) cc_final: 0.7674 (tpp) REVERT: R 268 MET cc_start: 0.7659 (tmm) cc_final: 0.7272 (tmm) REVERT: S 222 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6851 (mm-30) REVERT: S 232 LYS cc_start: 0.7913 (tptm) cc_final: 0.7446 (tptm) outliers start: 57 outliers final: 41 residues processed: 304 average time/residue: 0.2685 time to fit residues: 106.1925 Evaluate side-chains 318 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 273 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 255 GLU Chi-restraints excluded: chain R residue 272 TYR Chi-restraints excluded: chain R residue 286 LYS Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 68 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 97 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.157746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.133677 restraints weight = 14592.702| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.65 r_work: 0.3553 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9177 Z= 0.247 Angle : 0.595 7.740 12421 Z= 0.309 Chirality : 0.043 0.209 1416 Planarity : 0.004 0.063 1547 Dihedral : 5.546 88.935 1290 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 5.49 % Allowed : 26.83 % Favored : 67.68 % 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: 0.65 (0.26), residues: 1118 helix: 2.46 (0.25), residues: 425 sheet: -0.98 (0.29), residues: 290 loop : -0.61 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.003 0.001 HIS B 225 PHE 0.052 0.002 PHE A 189 TYR 0.035 0.002 TYR S 223 ARG 0.007 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 268 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 THR cc_start: 0.8113 (t) cc_final: 0.7884 (t) REVERT: A 192 LYS cc_start: 0.8125 (mttp) cc_final: 0.7838 (mmtp) REVERT: A 219 THR cc_start: 0.8353 (p) cc_final: 0.7984 (t) REVERT: A 232 MET cc_start: 0.6780 (mmm) cc_final: 0.6323 (mmm) REVERT: A 242 ARG cc_start: 0.7837 (mtt180) cc_final: 0.7534 (mtt180) REVERT: A 245 GLU cc_start: 0.8012 (tp30) cc_final: 0.7662 (tp30) REVERT: A 274 PHE cc_start: 0.7041 (t80) cc_final: 0.6719 (t80) REVERT: A 305 ASN cc_start: 0.7799 (m110) cc_final: 0.7480 (m110) REVERT: A 317 LYS cc_start: 0.7731 (ptmm) cc_final: 0.7257 (ptmm) REVERT: A 346 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7416 (tm-30) REVERT: B 15 LYS cc_start: 0.8946 (mtpt) cc_final: 0.8613 (mtpt) REVERT: B 55 LEU cc_start: 0.8449 (mm) cc_final: 0.8130 (mp) REVERT: B 68 ARG cc_start: 0.5826 (ttp-170) cc_final: 0.5444 (ttt-90) REVERT: B 129 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6679 (mmm-85) REVERT: B 153 ASP cc_start: 0.6730 (m-30) cc_final: 0.6398 (m-30) REVERT: B 159 THR cc_start: 0.7660 (OUTLIER) cc_final: 0.7353 (p) REVERT: B 196 THR cc_start: 0.7827 (p) cc_final: 0.7502 (p) REVERT: B 197 ARG cc_start: 0.7311 (mtp85) cc_final: 0.6993 (mtp-110) REVERT: B 214 ARG cc_start: 0.7431 (mtp85) cc_final: 0.7094 (mtp85) REVERT: B 258 ASP cc_start: 0.6346 (t0) cc_final: 0.6112 (t0) REVERT: B 284 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8049 (tp) REVERT: B 314 ARG cc_start: 0.7673 (mtp180) cc_final: 0.7192 (ttm-80) REVERT: C 21 MET cc_start: 0.7389 (mmm) cc_final: 0.6972 (mmm) REVERT: C 22 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6832 (mp0) REVERT: R 81 MET cc_start: 0.8076 (tmm) cc_final: 0.7734 (tmm) REVERT: R 108 PHE cc_start: 0.8394 (t80) cc_final: 0.8158 (t80) REVERT: R 125 ARG cc_start: 0.7861 (mtt180) cc_final: 0.7394 (mtt180) REVERT: R 140 PHE cc_start: 0.7718 (OUTLIER) cc_final: 0.7264 (t80) REVERT: R 143 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6586 (tt) REVERT: R 147 LEU cc_start: 0.6796 (pp) cc_final: 0.6302 (tt) REVERT: R 205 MET cc_start: 0.8207 (tpp) cc_final: 0.7683 (tpp) REVERT: R 268 MET cc_start: 0.7647 (tmm) cc_final: 0.7238 (tmm) REVERT: S 179 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7152 (mpt-90) REVERT: S 222 GLU cc_start: 0.7304 (mm-30) cc_final: 0.6808 (mm-30) outliers start: 54 outliers final: 37 residues processed: 301 average time/residue: 0.2666 time to fit residues: 103.8193 Evaluate side-chains 313 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 269 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 255 GLU Chi-restraints excluded: chain R residue 272 TYR Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 179 ARG Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 104 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 47 optimal weight: 0.0570 chunk 3 optimal weight: 0.3980 chunk 89 optimal weight: 0.5980 chunk 67 optimal weight: 0.0770 chunk 99 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 293 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.159917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.136261 restraints weight = 14295.575| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.60 r_work: 0.3591 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9177 Z= 0.175 Angle : 0.585 8.391 12421 Z= 0.302 Chirality : 0.042 0.196 1416 Planarity : 0.004 0.066 1547 Dihedral : 5.330 87.958 1290 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.88 % Allowed : 27.85 % Favored : 67.28 % 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: 0.75 (0.26), residues: 1118 helix: 2.55 (0.25), residues: 425 sheet: -0.92 (0.29), residues: 288 loop : -0.58 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.002 0.001 HIS S 35 PHE 0.058 0.002 PHE A 189 TYR 0.032 0.002 TYR S 223 ARG 0.007 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 260 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 THR cc_start: 0.8098 (t) cc_final: 0.7868 (t) REVERT: A 50 LYS cc_start: 0.7893 (ttmm) cc_final: 0.7514 (mtpp) REVERT: A 192 LYS cc_start: 0.8150 (mttp) cc_final: 0.7894 (mmtp) REVERT: A 219 THR cc_start: 0.8295 (p) cc_final: 0.7912 (t) REVERT: A 232 MET cc_start: 0.6731 (mmm) cc_final: 0.6367 (mmm) REVERT: A 242 ARG cc_start: 0.7756 (mtt180) cc_final: 0.7482 (mtt180) REVERT: A 245 GLU cc_start: 0.7975 (tp30) cc_final: 0.7643 (tp30) REVERT: A 274 PHE cc_start: 0.7023 (t80) cc_final: 0.6706 (t80) REVERT: A 317 LYS cc_start: 0.7702 (ptmm) cc_final: 0.7285 (ttpp) REVERT: A 346 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7405 (tm-30) REVERT: B 15 LYS cc_start: 0.8948 (mtpt) cc_final: 0.8620 (mtpt) REVERT: B 68 ARG cc_start: 0.5772 (ttp-170) cc_final: 0.4973 (ttp-170) REVERT: B 153 ASP cc_start: 0.6738 (m-30) cc_final: 0.6413 (m-30) REVERT: B 196 THR cc_start: 0.7742 (p) cc_final: 0.7441 (p) REVERT: B 197 ARG cc_start: 0.7230 (mtp85) cc_final: 0.6969 (mtp85) REVERT: B 214 ARG cc_start: 0.7296 (mtp85) cc_final: 0.6956 (mtp85) REVERT: B 258 ASP cc_start: 0.6267 (t0) cc_final: 0.6040 (t0) REVERT: B 284 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8049 (tp) REVERT: C 22 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6672 (mp0) REVERT: C 27 ARG cc_start: 0.7050 (mtm-85) cc_final: 0.6626 (mmt90) REVERT: R 37 LYS cc_start: 0.7478 (pttp) cc_final: 0.7149 (pptt) REVERT: R 108 PHE cc_start: 0.8376 (t80) cc_final: 0.8070 (t80) REVERT: R 125 ARG cc_start: 0.7888 (mtt180) cc_final: 0.7418 (mtt180) REVERT: R 140 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.7267 (t80) REVERT: R 143 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.6572 (tt) REVERT: R 147 LEU cc_start: 0.6786 (pp) cc_final: 0.6279 (tt) REVERT: R 205 MET cc_start: 0.8229 (tpp) cc_final: 0.7644 (tpp) REVERT: R 268 MET cc_start: 0.7547 (tmm) cc_final: 0.7148 (tmm) REVERT: S 179 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7166 (mpt-90) REVERT: S 222 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6792 (mm-30) outliers start: 48 outliers final: 35 residues processed: 289 average time/residue: 0.2742 time to fit residues: 102.5875 Evaluate side-chains 304 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 264 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 255 GLU Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 179 ARG Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 72 optimal weight: 1.9990 chunk 103 optimal weight: 0.0970 chunk 74 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 100 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.159646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.135929 restraints weight = 14407.823| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.63 r_work: 0.3573 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9177 Z= 0.219 Angle : 0.603 9.110 12421 Z= 0.313 Chirality : 0.043 0.211 1416 Planarity : 0.004 0.064 1547 Dihedral : 5.386 87.910 1290 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.88 % Allowed : 27.64 % Favored : 67.48 % 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: 0.68 (0.26), residues: 1118 helix: 2.49 (0.25), residues: 431 sheet: -0.94 (0.29), residues: 290 loop : -0.68 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 89 HIS 0.002 0.001 HIS B 54 PHE 0.054 0.002 PHE A 189 TYR 0.033 0.002 TYR S 223 ARG 0.007 0.000 ARG A 36 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 275 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 THR cc_start: 0.8089 (t) cc_final: 0.7879 (t) REVERT: A 50 LYS cc_start: 0.7926 (ttmm) cc_final: 0.7543 (mtpp) REVERT: A 61 LYS cc_start: 0.6776 (mtmt) cc_final: 0.6375 (ttpp) REVERT: A 192 LYS cc_start: 0.8137 (mttp) cc_final: 0.7869 (mmtp) REVERT: A 219 THR cc_start: 0.8315 (p) cc_final: 0.7945 (t) REVERT: A 232 MET cc_start: 0.6771 (mmm) cc_final: 0.6357 (mmm) REVERT: A 242 ARG cc_start: 0.7807 (mtt180) cc_final: 0.7526 (mtt180) REVERT: A 245 GLU cc_start: 0.7970 (tp30) cc_final: 0.7632 (tp30) REVERT: A 274 PHE cc_start: 0.7024 (t80) cc_final: 0.6724 (t80) REVERT: A 317 LYS cc_start: 0.7711 (ptmm) cc_final: 0.7222 (ptmm) REVERT: A 346 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7437 (tm-30) REVERT: B 15 LYS cc_start: 0.8951 (mtpt) cc_final: 0.8622 (mtpt) REVERT: B 68 ARG cc_start: 0.5792 (ttp-170) cc_final: 0.4973 (ttp-170) REVERT: B 110 ASN cc_start: 0.7910 (m-40) cc_final: 0.7696 (m-40) REVERT: B 153 ASP cc_start: 0.6781 (m-30) cc_final: 0.6434 (m-30) REVERT: B 196 THR cc_start: 0.7753 (p) cc_final: 0.7466 (p) REVERT: B 197 ARG cc_start: 0.7278 (mtp85) cc_final: 0.7003 (mtp85) REVERT: B 214 ARG cc_start: 0.7325 (mtp85) cc_final: 0.6974 (mtp85) REVERT: B 219 ARG cc_start: 0.7427 (mmt-90) cc_final: 0.7158 (mmt90) REVERT: B 284 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8040 (tp) REVERT: B 314 ARG cc_start: 0.7563 (mtp180) cc_final: 0.7289 (ttm-80) REVERT: C 22 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6516 (mp0) REVERT: C 27 ARG cc_start: 0.7063 (mtm-85) cc_final: 0.6665 (mmt90) REVERT: R 37 LYS cc_start: 0.7541 (pttp) cc_final: 0.7185 (pptt) REVERT: R 81 MET cc_start: 0.7997 (tmm) cc_final: 0.7705 (tmm) REVERT: R 125 ARG cc_start: 0.7849 (mtt180) cc_final: 0.7393 (mtt180) REVERT: R 140 PHE cc_start: 0.7689 (OUTLIER) cc_final: 0.7280 (t80) REVERT: R 143 LEU cc_start: 0.6803 (OUTLIER) cc_final: 0.6549 (tt) REVERT: R 147 LEU cc_start: 0.6799 (pp) cc_final: 0.6297 (tt) REVERT: R 205 MET cc_start: 0.8244 (tpp) cc_final: 0.7644 (tpp) REVERT: R 268 MET cc_start: 0.7546 (tmm) cc_final: 0.7154 (tmm) REVERT: S 179 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7107 (mpt-90) REVERT: S 222 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6822 (mm-30) outliers start: 48 outliers final: 37 residues processed: 303 average time/residue: 0.2634 time to fit residues: 103.5479 Evaluate side-chains 308 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 266 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 255 GLU Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 179 ARG Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 20 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 110 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 293 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.158911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.134801 restraints weight = 14336.580| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.65 r_work: 0.3568 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9177 Z= 0.253 Angle : 0.626 11.675 12421 Z= 0.324 Chirality : 0.043 0.197 1416 Planarity : 0.004 0.064 1547 Dihedral : 5.479 88.209 1290 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.78 % Allowed : 27.95 % Favored : 67.28 % 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: 0.63 (0.26), residues: 1118 helix: 2.45 (0.25), residues: 430 sheet: -0.91 (0.29), residues: 289 loop : -0.75 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP R 89 HIS 0.003 0.001 HIS B 225 PHE 0.053 0.002 PHE A 189 TYR 0.035 0.002 TYR S 223 ARG 0.007 0.000 ARG A 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4727.42 seconds wall clock time: 85 minutes 6.45 seconds (5106.45 seconds total)