Starting phenix.real_space_refine on Sat Aug 3 21:53:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xqp_38584/08_2024/8xqp_38584.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xqp_38584/08_2024/8xqp_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xqp_38584/08_2024/8xqp_38584.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xqp_38584/08_2024/8xqp_38584.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xqp_38584/08_2024/8xqp_38584.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xqp_38584/08_2024/8xqp_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 Residue "A GLU 43": "OE1" <-> "OE2" Residue "S ARG 98": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 5.68, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 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: 3.85 Conformation dependent library (CDL) restraints added in 1.5 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: 1.12 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: 3.05 Time building geometry restraints manager: 4.13 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: 99.11 - 106.11: 132 106.11 - 113.12: 5050 113.12 - 120.12: 3148 120.12 - 127.12: 4001 127.12 - 134.12: 90 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: 1.120 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: 29.610 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.170 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 3 poor density : 276 time to evaluate : 0.955 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: 0.2541 time to fit residues: 91.7895 Evaluate side-chains 278 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 275 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 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 fitting. rotamer outliers: 38 poor density : 267 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: A 28 VAL cc_start: 0.8426 (t) cc_final: 0.8208 (t) REVERT: A 192 LYS cc_start: 0.8178 (mttp) cc_final: 0.7948 (mmtp) REVERT: A 201 VAL cc_start: 0.7613 (OUTLIER) cc_final: 0.7374 (t) REVERT: A 219 THR cc_start: 0.8454 (p) cc_final: 0.8170 (t) REVERT: A 317 LYS cc_start: 0.7839 (ptmm) cc_final: 0.7514 (ptmm) REVERT: B 15 LYS cc_start: 0.8918 (mtpt) cc_final: 0.8595 (mtpt) REVERT: B 68 ARG cc_start: 0.5876 (ttp-170) cc_final: 0.5290 (ttp-170) REVERT: B 129 ARG cc_start: 0.6789 (OUTLIER) cc_final: 0.6557 (mmp80) REVERT: B 196 THR cc_start: 0.7934 (p) cc_final: 0.7672 (p) REVERT: B 209 LYS cc_start: 0.8456 (mttm) cc_final: 0.8084 (mttm) REVERT: B 210 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7775 (tp) REVERT: B 214 ARG cc_start: 0.7235 (mtp85) cc_final: 0.5934 (mtp85) REVERT: B 217 MET cc_start: 0.6545 (ppp) cc_final: 0.5873 (ppp) REVERT: C 22 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.7049 (mp0) REVERT: C 27 ARG cc_start: 0.7016 (mtm-85) cc_final: 0.6562 (mmt90) REVERT: R 65 SER cc_start: 0.8932 (OUTLIER) cc_final: 0.8688 (m) REVERT: R 125 ARG cc_start: 0.7735 (mtt180) cc_final: 0.7301 (mtt180) REVERT: R 147 LEU cc_start: 0.6654 (pp) cc_final: 0.6082 (tt) REVERT: R 205 MET cc_start: 0.8355 (tpp) cc_final: 0.7818 (tpp) REVERT: S 157 ASN cc_start: 0.8294 (p0) cc_final: 0.7997 (p0) outliers start: 38 outliers final: 16 residues processed: 288 average time/residue: 0.2558 time to fit residues: 95.9596 Evaluate side-chains 280 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 259 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.0040 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 0.0270 chunk 109 optimal weight: 0.0040 chunk 89 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.2662 ------------------------------------------------------------------------------- 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 ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9177 Z= 0.164 Angle : 0.556 9.055 12421 Z= 0.290 Chirality : 0.041 0.211 1416 Planarity : 0.005 0.063 1547 Dihedral : 5.594 85.293 1292 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.17 % Allowed : 25.71 % 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: 0.62 (0.26), residues: 1118 helix: 2.35 (0.25), residues: 429 sheet: -0.87 (0.30), residues: 288 loop : -0.68 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.003 0.001 HIS B 54 PHE 0.018 0.001 PHE A 196 TYR 0.032 0.001 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 315 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 274 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 VAL cc_start: 0.8428 (t) cc_final: 0.8183 (t) REVERT: A 61 LYS cc_start: 0.6703 (mtmt) cc_final: 0.6416 (ttpp) REVERT: A 192 LYS cc_start: 0.8180 (mttp) cc_final: 0.7919 (mmtp) REVERT: A 210 LYS cc_start: 0.6354 (mptp) cc_final: 0.6135 (mptp) REVERT: A 242 ARG cc_start: 0.7341 (mtt180) cc_final: 0.6769 (mtt-85) REVERT: A 245 GLU cc_start: 0.8094 (tp30) cc_final: 0.7850 (tp30) REVERT: A 317 LYS cc_start: 0.7824 (ptmm) cc_final: 0.7418 (ttpp) REVERT: B 15 LYS cc_start: 0.8942 (mtpt) cc_final: 0.8595 (mtpt) REVERT: B 68 ARG cc_start: 0.5828 (ttp-170) cc_final: 0.5346 (ttt-90) REVERT: B 159 THR cc_start: 0.7694 (m) cc_final: 0.7260 (p) REVERT: B 196 THR cc_start: 0.7916 (p) cc_final: 0.7649 (p) REVERT: B 209 LYS cc_start: 0.8552 (mttm) cc_final: 0.8322 (mttp) REVERT: B 210 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7629 (tp) REVERT: C 27 ARG cc_start: 0.7007 (mtm-85) cc_final: 0.6527 (mmt90) REVERT: R 65 SER cc_start: 0.8916 (OUTLIER) cc_final: 0.8660 (m) REVERT: R 99 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8486 (tp) REVERT: R 125 ARG cc_start: 0.7710 (mtt180) cc_final: 0.7271 (mtt180) REVERT: R 147 LEU cc_start: 0.6639 (pp) cc_final: 0.6019 (tt) REVERT: R 205 MET cc_start: 0.8304 (tpp) cc_final: 0.7737 (tpp) REVERT: R 268 MET cc_start: 0.7571 (tmm) cc_final: 0.7205 (tmm) REVERT: S 157 ASN cc_start: 0.8270 (p0) cc_final: 0.8040 (p0) outliers start: 41 outliers final: 25 residues processed: 301 average time/residue: 0.2593 time to fit residues: 101.4901 Evaluate side-chains 297 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 269 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 253 ILE 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 129 ARG 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 R residue 59 VAL Chi-restraints excluded: chain R residue 65 SER 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 75 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 220 GLN B 293 ASN B 340 ASN S 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9177 Z= 0.342 Angle : 0.610 7.664 12421 Z= 0.323 Chirality : 0.044 0.239 1416 Planarity : 0.005 0.064 1547 Dihedral : 5.813 89.064 1292 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.98 % Allowed : 25.41 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.26), residues: 1118 helix: 2.27 (0.25), residues: 431 sheet: -0.99 (0.29), residues: 298 loop : -0.72 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.004 0.001 HIS B 225 PHE 0.017 0.002 PHE A 196 TYR 0.034 0.002 TYR S 223 ARG 0.007 0.001 ARG B 134 *********************** 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 319 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 270 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 LYS cc_start: 0.8061 (mttp) cc_final: 0.7806 (mmtp) REVERT: A 201 VAL cc_start: 0.7720 (OUTLIER) cc_final: 0.7507 (t) REVERT: A 219 THR cc_start: 0.8433 (p) cc_final: 0.8121 (t) REVERT: A 242 ARG cc_start: 0.7529 (mtt180) cc_final: 0.7276 (mtt180) REVERT: A 245 GLU cc_start: 0.8126 (tp30) cc_final: 0.7838 (tp30) REVERT: A 274 PHE cc_start: 0.6975 (t80) cc_final: 0.6624 (t80) REVERT: A 305 ASN cc_start: 0.7678 (m110) cc_final: 0.7150 (m110) REVERT: A 317 LYS cc_start: 0.7865 (ptmm) cc_final: 0.7429 (ttpp) REVERT: A 346 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7570 (tm-30) REVERT: B 15 LYS cc_start: 0.8948 (mtpt) cc_final: 0.8607 (mtpt) REVERT: B 68 ARG cc_start: 0.5812 (ttp-170) cc_final: 0.5393 (ttt-90) REVERT: B 196 THR cc_start: 0.7800 (p) cc_final: 0.7546 (p) REVERT: B 209 LYS cc_start: 0.8604 (mttm) cc_final: 0.8396 (mttp) REVERT: B 210 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7566 (tp) REVERT: B 212 ASP cc_start: 0.8154 (p0) cc_final: 0.7821 (p0) REVERT: B 214 ARG cc_start: 0.7093 (mtp85) cc_final: 0.6893 (mtp85) REVERT: B 219 ARG cc_start: 0.7347 (mmt90) cc_final: 0.7084 (mmt90) REVERT: B 291 ASP cc_start: 0.6901 (p0) cc_final: 0.6676 (p0) REVERT: C 21 MET cc_start: 0.7704 (mmm) cc_final: 0.7293 (mmm) REVERT: C 22 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7160 (mp0) REVERT: C 27 ARG cc_start: 0.7105 (mtm-85) cc_final: 0.6342 (mmt90) REVERT: R 66 TRP cc_start: 0.7502 (t60) cc_final: 0.7184 (t60) REVERT: R 85 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7671 (pp) REVERT: R 125 ARG cc_start: 0.7773 (mtt180) cc_final: 0.7320 (mtt180) REVERT: R 147 LEU cc_start: 0.6853 (pp) cc_final: 0.6300 (tt) REVERT: R 205 MET cc_start: 0.8368 (tpp) cc_final: 0.7918 (tpp) REVERT: R 268 MET cc_start: 0.7650 (tmm) cc_final: 0.7387 (tmm) REVERT: S 222 GLU cc_start: 0.7304 (mm-30) cc_final: 0.6926 (mm-30) REVERT: S 232 LYS cc_start: 0.8013 (tptm) cc_final: 0.7575 (tptm) outliers start: 49 outliers final: 37 residues processed: 296 average time/residue: 0.2526 time to fit residues: 97.3479 Evaluate side-chains 305 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 264 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 190 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 52 ARG 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 218 CYS Chi-restraints excluded: chain B residue 228 ASP 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 18 GLN Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain R residue 59 VAL Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 215 THR 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 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 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 1 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.1766 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= 0.251 Angle : 0.579 7.140 12421 Z= 0.304 Chirality : 0.042 0.229 1416 Planarity : 0.004 0.062 1547 Dihedral : 5.729 88.762 1292 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.49 % Allowed : 25.71 % Favored : 68.80 % 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: 0.62 (0.26), residues: 1118 helix: 2.43 (0.26), residues: 425 sheet: -0.98 (0.29), residues: 292 loop : -0.63 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 169 HIS 0.003 0.001 HIS B 266 PHE 0.029 0.002 PHE A 189 TYR 0.034 0.002 TYR S 223 ARG 0.008 0.000 ARG B 134 *********************** 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 319 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 265 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 61 LYS cc_start: 0.6833 (mtmt) cc_final: 0.6551 (ttpp) REVERT: A 192 LYS cc_start: 0.8046 (mttp) cc_final: 0.7793 (mmtp) REVERT: A 219 THR cc_start: 0.8443 (p) cc_final: 0.8113 (t) REVERT: A 242 ARG cc_start: 0.7544 (mtt180) cc_final: 0.7262 (mtt180) REVERT: A 245 GLU cc_start: 0.8118 (tp30) cc_final: 0.7819 (tp30) REVERT: A 274 PHE cc_start: 0.6965 (t80) cc_final: 0.6614 (t80) REVERT: A 317 LYS cc_start: 0.7838 (ptmm) cc_final: 0.7425 (ttpp) REVERT: A 346 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7560 (tm-30) REVERT: B 68 ARG cc_start: 0.5808 (ttp-170) cc_final: 0.5392 (ttt-90) REVERT: B 129 ARG cc_start: 0.6836 (OUTLIER) cc_final: 0.6584 (mmp80) REVERT: B 130 GLU cc_start: 0.7371 (mp0) cc_final: 0.6469 (mp0) REVERT: B 196 THR cc_start: 0.7839 (p) cc_final: 0.7585 (p) REVERT: B 209 LYS cc_start: 0.8641 (mttm) cc_final: 0.8413 (mttp) REVERT: B 210 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7773 (tp) REVERT: B 284 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8077 (tp) REVERT: R 37 LYS cc_start: 0.7632 (pttp) cc_final: 0.7311 (pptt) REVERT: R 66 TRP cc_start: 0.7494 (t60) cc_final: 0.7141 (t60) REVERT: R 99 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8558 (tp) REVERT: R 125 ARG cc_start: 0.7711 (mtt180) cc_final: 0.7228 (mtt180) REVERT: R 140 PHE cc_start: 0.7625 (OUTLIER) cc_final: 0.7222 (t80) REVERT: R 147 LEU cc_start: 0.6848 (pp) cc_final: 0.6272 (tt) REVERT: R 205 MET cc_start: 0.8282 (tpp) cc_final: 0.7698 (tpp) REVERT: R 268 MET cc_start: 0.7614 (tmm) cc_final: 0.7377 (tmm) REVERT: S 133 SER cc_start: 0.5348 (t) cc_final: 0.5143 (p) REVERT: S 222 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6897 (mm-30) REVERT: S 232 LYS cc_start: 0.8000 (tptm) cc_final: 0.7540 (tptm) outliers start: 54 outliers final: 33 residues processed: 296 average time/residue: 0.2500 time to fit residues: 96.3926 Evaluate side-chains 308 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 270 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 190 SER Chi-restraints excluded: chain A residue 212 ILE 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 81 ILE 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 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 18 GLN 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 272 TYR 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 180 MET 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 62 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 chunk 107 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9177 Z= 0.237 Angle : 0.582 8.796 12421 Z= 0.306 Chirality : 0.042 0.214 1416 Planarity : 0.004 0.064 1547 Dihedral : 5.710 88.494 1292 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.88 % Allowed : 26.83 % Favored : 68.29 % 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: 0.62 (0.26), residues: 1118 helix: 2.41 (0.25), residues: 425 sheet: -1.00 (0.29), residues: 290 loop : -0.60 (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 0.020 0.001 PHE A 196 TYR 0.034 0.002 TYR S 223 ARG 0.008 0.000 ARG B 134 *********************** 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 325 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 277 time to evaluate : 1.210 Fit side-chains revert: symmetry clash REVERT: A 28 VAL cc_start: 0.8443 (t) cc_final: 0.8239 (t) REVERT: A 48 THR cc_start: 0.8178 (t) cc_final: 0.7952 (t) REVERT: A 192 LYS cc_start: 0.8042 (mttp) cc_final: 0.7788 (mmtp) REVERT: A 242 ARG cc_start: 0.7555 (mtt180) cc_final: 0.7328 (mtt180) REVERT: A 245 GLU cc_start: 0.8120 (tp30) cc_final: 0.7785 (tp30) REVERT: A 274 PHE cc_start: 0.6992 (t80) cc_final: 0.6644 (t80) REVERT: A 317 LYS cc_start: 0.7843 (ptmm) cc_final: 0.7413 (ttpp) REVERT: A 346 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7556 (tm-30) REVERT: B 15 LYS cc_start: 0.8936 (mtpt) cc_final: 0.8546 (mtpt) REVERT: B 68 ARG cc_start: 0.5803 (ttp-170) cc_final: 0.5365 (ttt-90) REVERT: B 130 GLU cc_start: 0.7367 (mp0) cc_final: 0.6299 (mp0) REVERT: B 134 ARG cc_start: 0.7083 (ptt-90) cc_final: 0.5854 (ptt-90) REVERT: B 196 THR cc_start: 0.7836 (p) cc_final: 0.7581 (p) REVERT: B 210 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7886 (tp) REVERT: B 212 ASP cc_start: 0.8184 (p0) cc_final: 0.7929 (p0) REVERT: B 266 HIS cc_start: 0.7574 (t70) cc_final: 0.7327 (t70) REVERT: B 284 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8069 (tp) REVERT: C 22 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: R 66 TRP cc_start: 0.7470 (t60) cc_final: 0.7108 (t60) REVERT: R 99 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8546 (tp) REVERT: R 125 ARG cc_start: 0.7710 (mtt180) cc_final: 0.7325 (mtt180) REVERT: R 140 PHE cc_start: 0.7613 (OUTLIER) cc_final: 0.7241 (t80) REVERT: R 143 LEU cc_start: 0.6798 (OUTLIER) cc_final: 0.6552 (tt) REVERT: R 147 LEU cc_start: 0.6863 (pp) cc_final: 0.6300 (tt) REVERT: R 205 MET cc_start: 0.8284 (tpp) cc_final: 0.7686 (tpp) REVERT: R 268 MET cc_start: 0.7606 (tmm) cc_final: 0.7231 (tmm) REVERT: S 222 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6867 (mm-30) REVERT: S 232 LYS cc_start: 0.7993 (tptm) cc_final: 0.7540 (tptm) outliers start: 48 outliers final: 35 residues processed: 304 average time/residue: 0.2470 time to fit residues: 98.6775 Evaluate side-chains 313 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 272 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 212 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 74 SER Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 95 LEU 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 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 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 129 THR 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 78 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2015 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= 0.256 Angle : 0.593 7.449 12421 Z= 0.312 Chirality : 0.043 0.214 1416 Planarity : 0.004 0.064 1547 Dihedral : 5.531 88.792 1290 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 5.08 % Allowed : 26.93 % Favored : 67.99 % 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: 0.62 (0.26), residues: 1118 helix: 2.42 (0.25), residues: 425 sheet: -1.01 (0.29), residues: 290 loop : -0.59 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.003 0.001 HIS B 266 PHE 0.033 0.002 PHE A 189 TYR 0.035 0.002 TYR S 223 ARG 0.009 0.001 ARG B 134 *********************** 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 325 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 275 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 THR cc_start: 0.8206 (t) cc_final: 0.8005 (t) REVERT: A 192 LYS cc_start: 0.8030 (mttp) cc_final: 0.7773 (mmtp) REVERT: A 219 THR cc_start: 0.8443 (p) cc_final: 0.8119 (t) REVERT: A 242 ARG cc_start: 0.7609 (mtt180) cc_final: 0.7313 (mtt180) REVERT: A 245 GLU cc_start: 0.8115 (tp30) cc_final: 0.7787 (tp30) REVERT: A 274 PHE cc_start: 0.6999 (t80) cc_final: 0.6664 (t80) REVERT: A 317 LYS cc_start: 0.7835 (ptmm) cc_final: 0.7370 (ptmm) REVERT: A 346 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7563 (tm-30) REVERT: B 15 LYS cc_start: 0.8915 (mtpt) cc_final: 0.8561 (mtpt) REVERT: B 68 ARG cc_start: 0.5796 (ttp-170) cc_final: 0.5391 (ttt-90) REVERT: B 130 GLU cc_start: 0.7392 (mp0) cc_final: 0.6589 (mp0) REVERT: B 196 THR cc_start: 0.7850 (p) cc_final: 0.7589 (p) REVERT: B 209 LYS cc_start: 0.8451 (mttp) cc_final: 0.8235 (mttp) REVERT: B 210 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7768 (tp) REVERT: B 258 ASP cc_start: 0.6537 (t0) cc_final: 0.6326 (t0) REVERT: B 266 HIS cc_start: 0.7470 (t70) cc_final: 0.7249 (t70) REVERT: B 284 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8080 (tp) REVERT: C 21 MET cc_start: 0.7708 (mmm) cc_final: 0.7250 (mmm) REVERT: C 22 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: R 37 LYS cc_start: 0.7606 (pttp) cc_final: 0.7345 (pptt) REVERT: R 66 TRP cc_start: 0.7488 (t60) cc_final: 0.7130 (t60) REVERT: R 99 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8556 (tp) REVERT: R 125 ARG cc_start: 0.7696 (mtt180) cc_final: 0.7288 (mtt180) REVERT: R 140 PHE cc_start: 0.7622 (OUTLIER) cc_final: 0.7247 (t80) REVERT: R 143 LEU cc_start: 0.6842 (OUTLIER) cc_final: 0.6592 (tt) REVERT: R 147 LEU cc_start: 0.6849 (pp) cc_final: 0.6274 (tt) REVERT: R 191 PHE cc_start: 0.6623 (t80) cc_final: 0.6418 (t80) REVERT: R 205 MET cc_start: 0.8287 (tpp) cc_final: 0.7698 (tpp) REVERT: R 268 MET cc_start: 0.7561 (tmm) cc_final: 0.7177 (tmm) REVERT: S 222 GLU cc_start: 0.7316 (mm-30) cc_final: 0.6922 (mm-30) REVERT: S 232 LYS cc_start: 0.7984 (tptm) cc_final: 0.7522 (tptm) outliers start: 50 outliers final: 33 residues processed: 301 average time/residue: 0.2476 time to fit residues: 97.1724 Evaluate side-chains 312 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 273 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 95 LEU 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 213 VAL 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 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 38 MET Chi-restraints excluded: chain C residue 51 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 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 129 THR 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 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 84 optimal weight: 0.0060 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9177 Z= 0.241 Angle : 0.593 7.561 12421 Z= 0.310 Chirality : 0.043 0.210 1416 Planarity : 0.004 0.064 1547 Dihedral : 5.488 88.961 1290 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 5.39 % Allowed : 26.83 % Favored : 67.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.26), residues: 1118 helix: 2.48 (0.26), residues: 425 sheet: -1.00 (0.29), residues: 290 loop : -0.59 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.002 0.001 HIS B 266 PHE 0.025 0.002 PHE A 189 TYR 0.034 0.002 TYR S 223 ARG 0.007 0.000 ARG B 134 *********************** 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 328 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 275 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: A 61 LYS cc_start: 0.6907 (mtmt) cc_final: 0.6693 (ttpp) REVERT: A 192 LYS cc_start: 0.8030 (mttp) cc_final: 0.7774 (mmtp) REVERT: A 199 PHE cc_start: 0.8322 (m-80) cc_final: 0.8113 (m-80) REVERT: A 242 ARG cc_start: 0.7624 (mtt180) cc_final: 0.7364 (mtt180) REVERT: A 245 GLU cc_start: 0.8110 (tp30) cc_final: 0.7784 (tp30) REVERT: A 274 PHE cc_start: 0.6999 (t80) cc_final: 0.6691 (t80) REVERT: A 305 ASN cc_start: 0.7762 (m110) cc_final: 0.7420 (m110) REVERT: A 317 LYS cc_start: 0.7826 (ptmm) cc_final: 0.7361 (ptmm) REVERT: A 346 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7563 (tm-30) REVERT: B 15 LYS cc_start: 0.8899 (mtpt) cc_final: 0.8559 (mtpt) REVERT: B 68 ARG cc_start: 0.5785 (ttp-170) cc_final: 0.5373 (ttt-90) REVERT: B 130 GLU cc_start: 0.7411 (mp0) cc_final: 0.6439 (mp0) REVERT: B 134 ARG cc_start: 0.7112 (ptt-90) cc_final: 0.5808 (ptt-90) REVERT: B 159 THR cc_start: 0.7685 (OUTLIER) cc_final: 0.7332 (p) REVERT: B 196 THR cc_start: 0.7834 (p) cc_final: 0.7580 (p) REVERT: B 210 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7734 (tp) REVERT: B 212 ASP cc_start: 0.8113 (p0) cc_final: 0.7717 (p0) REVERT: B 219 ARG cc_start: 0.7225 (mmt90) cc_final: 0.6996 (mmt90) REVERT: B 258 ASP cc_start: 0.6567 (t0) cc_final: 0.6290 (t0) REVERT: B 284 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8082 (tp) REVERT: B 314 ARG cc_start: 0.7773 (mtp180) cc_final: 0.7222 (ttm-80) REVERT: C 21 MET cc_start: 0.7712 (mmm) cc_final: 0.7244 (mmm) REVERT: C 22 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: R 66 TRP cc_start: 0.7510 (t60) cc_final: 0.7123 (t60) REVERT: R 99 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8528 (tp) REVERT: R 125 ARG cc_start: 0.7679 (mtt180) cc_final: 0.7296 (mtt180) REVERT: R 140 PHE cc_start: 0.7615 (OUTLIER) cc_final: 0.7224 (t80) REVERT: R 143 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6697 (tt) REVERT: R 147 LEU cc_start: 0.6823 (pp) cc_final: 0.6235 (tt) REVERT: R 191 PHE cc_start: 0.6645 (t80) cc_final: 0.6431 (t80) REVERT: R 205 MET cc_start: 0.8254 (tpp) cc_final: 0.7726 (tpp) REVERT: R 268 MET cc_start: 0.7541 (tmm) cc_final: 0.7155 (tmm) REVERT: S 222 GLU cc_start: 0.7320 (mm-30) cc_final: 0.6912 (mm-30) REVERT: S 232 LYS cc_start: 0.7982 (tptm) cc_final: 0.7503 (tptm) outliers start: 53 outliers final: 38 residues processed: 306 average time/residue: 0.2499 time to fit residues: 100.0970 Evaluate side-chains 318 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 273 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 212 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 95 LEU 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 159 THR Chi-restraints excluded: chain B residue 210 LEU 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 9 ILE Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 51 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 120 LEU 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 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 102 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 105 optimal weight: 0.4980 chunk 64 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 24 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9177 Z= 0.229 Angle : 0.616 9.398 12421 Z= 0.318 Chirality : 0.043 0.201 1416 Planarity : 0.004 0.064 1547 Dihedral : 5.468 88.484 1290 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 5.39 % Allowed : 26.52 % Favored : 68.09 % 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: 0.70 (0.26), residues: 1118 helix: 2.50 (0.25), residues: 425 sheet: -0.97 (0.28), residues: 290 loop : -0.56 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.002 0.001 HIS R 276 PHE 0.021 0.001 PHE A 189 TYR 0.034 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 329 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 276 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 61 LYS cc_start: 0.6891 (mtmt) cc_final: 0.6633 (ttpp) REVERT: A 192 LYS cc_start: 0.8027 (mttp) cc_final: 0.7772 (mmtp) REVERT: A 219 THR cc_start: 0.8419 (p) cc_final: 0.8103 (t) REVERT: A 242 ARG cc_start: 0.7635 (mtt180) cc_final: 0.7416 (mtt180) REVERT: A 245 GLU cc_start: 0.8088 (tp30) cc_final: 0.7774 (tp30) REVERT: A 274 PHE cc_start: 0.6982 (t80) cc_final: 0.6714 (t80) REVERT: A 305 ASN cc_start: 0.7746 (m110) cc_final: 0.7429 (m110) REVERT: A 317 LYS cc_start: 0.7816 (ptmm) cc_final: 0.7366 (ptmm) REVERT: A 346 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7587 (tm-30) REVERT: B 15 LYS cc_start: 0.8902 (mtpt) cc_final: 0.8554 (mtpt) REVERT: B 68 ARG cc_start: 0.5778 (ttp-170) cc_final: 0.5379 (ttt-90) REVERT: B 130 GLU cc_start: 0.7417 (mp0) cc_final: 0.6377 (mp0) REVERT: B 134 ARG cc_start: 0.7105 (ptt-90) cc_final: 0.5798 (ptt-90) REVERT: B 159 THR cc_start: 0.7652 (OUTLIER) cc_final: 0.7326 (p) REVERT: B 176 GLN cc_start: 0.7991 (mt0) cc_final: 0.7788 (mt0) REVERT: B 196 THR cc_start: 0.7791 (p) cc_final: 0.7539 (p) REVERT: B 209 LYS cc_start: 0.8436 (mttp) cc_final: 0.8179 (mttm) REVERT: B 210 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7725 (tp) REVERT: B 212 ASP cc_start: 0.8098 (p0) cc_final: 0.7661 (p0) REVERT: B 219 ARG cc_start: 0.7229 (mmt90) cc_final: 0.6984 (mmt90) REVERT: B 220 GLN cc_start: 0.7919 (mt0) cc_final: 0.7657 (mt0) REVERT: B 258 ASP cc_start: 0.6481 (t0) cc_final: 0.6238 (t0) REVERT: B 284 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8073 (tp) REVERT: B 314 ARG cc_start: 0.7752 (mtp180) cc_final: 0.7242 (ttm-80) REVERT: C 22 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: R 37 LYS cc_start: 0.7569 (pttp) cc_final: 0.7248 (pptt) REVERT: R 99 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8534 (tp) REVERT: R 125 ARG cc_start: 0.7672 (mtt180) cc_final: 0.7294 (mtt180) REVERT: R 140 PHE cc_start: 0.7605 (OUTLIER) cc_final: 0.7220 (t80) REVERT: R 143 LEU cc_start: 0.6866 (OUTLIER) cc_final: 0.6610 (tt) REVERT: R 147 LEU cc_start: 0.6838 (pp) cc_final: 0.6232 (tp) REVERT: R 191 PHE cc_start: 0.6638 (t80) cc_final: 0.6425 (t80) REVERT: R 205 MET cc_start: 0.8275 (tpp) cc_final: 0.7699 (tpp) REVERT: R 268 MET cc_start: 0.7533 (tmm) cc_final: 0.7144 (tmm) REVERT: S 222 GLU cc_start: 0.7314 (mm-30) cc_final: 0.6908 (mm-30) outliers start: 53 outliers final: 41 residues processed: 307 average time/residue: 0.2404 time to fit residues: 96.4617 Evaluate side-chains 318 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 270 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 212 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 18 ILE 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 95 LEU 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 159 THR Chi-restraints excluded: chain B residue 210 LEU 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 9 ILE Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 51 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 120 LEU 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 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 50 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 0.3980 chunk 26 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.2216 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= 0.237 Angle : 0.634 11.700 12421 Z= 0.322 Chirality : 0.043 0.202 1416 Planarity : 0.004 0.065 1547 Dihedral : 5.469 88.236 1290 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.28 % Allowed : 26.73 % Favored : 67.99 % 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: 0.70 (0.26), residues: 1118 helix: 2.48 (0.25), residues: 425 sheet: -0.96 (0.29), residues: 290 loop : -0.55 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.002 0.001 HIS A 195 PHE 0.017 0.001 PHE A 196 TYR 0.034 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 324 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 272 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: A 48 THR cc_start: 0.8132 (t) cc_final: 0.7869 (t) REVERT: A 61 LYS cc_start: 0.6881 (mtmt) cc_final: 0.6235 (ttmt) REVERT: A 192 LYS cc_start: 0.8027 (mttp) cc_final: 0.7769 (mmtp) REVERT: A 199 PHE cc_start: 0.8328 (m-80) cc_final: 0.8116 (m-80) REVERT: A 230 TYR cc_start: 0.6837 (p90) cc_final: 0.6407 (p90) REVERT: A 242 ARG cc_start: 0.7658 (mtt180) cc_final: 0.7446 (mtt180) REVERT: A 245 GLU cc_start: 0.8089 (tp30) cc_final: 0.7767 (tp30) REVERT: A 274 PHE cc_start: 0.6967 (t80) cc_final: 0.6667 (t80) REVERT: A 305 ASN cc_start: 0.7712 (m110) cc_final: 0.7409 (m110) REVERT: A 317 LYS cc_start: 0.7816 (ptmm) cc_final: 0.7380 (ttpp) REVERT: A 346 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7572 (tm-30) REVERT: B 15 LYS cc_start: 0.8901 (mtpt) cc_final: 0.8550 (mtpt) REVERT: B 68 ARG cc_start: 0.5778 (ttp-170) cc_final: 0.5389 (ttt-90) REVERT: B 130 GLU cc_start: 0.7421 (mp0) cc_final: 0.6400 (mp0) REVERT: B 134 ARG cc_start: 0.7107 (ptt-90) cc_final: 0.5804 (ptt-90) REVERT: B 159 THR cc_start: 0.7657 (OUTLIER) cc_final: 0.7379 (p) REVERT: B 176 GLN cc_start: 0.8032 (mt0) cc_final: 0.7824 (mt0) REVERT: B 196 THR cc_start: 0.7787 (p) cc_final: 0.7535 (p) REVERT: B 209 LYS cc_start: 0.8435 (mttp) cc_final: 0.8182 (mttm) REVERT: B 210 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7790 (tp) REVERT: B 220 GLN cc_start: 0.7943 (mt0) cc_final: 0.7673 (mt0) REVERT: B 258 ASP cc_start: 0.6511 (t0) cc_final: 0.6256 (t0) REVERT: B 284 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8074 (tp) REVERT: C 21 MET cc_start: 0.7704 (mmm) cc_final: 0.7239 (mmm) REVERT: C 22 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: R 37 LYS cc_start: 0.7603 (pttp) cc_final: 0.7244 (pptt) REVERT: R 99 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8530 (tp) REVERT: R 125 ARG cc_start: 0.7674 (mtt180) cc_final: 0.7133 (mtt180) REVERT: R 140 PHE cc_start: 0.7608 (OUTLIER) cc_final: 0.7220 (t80) REVERT: R 143 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6702 (tt) REVERT: R 147 LEU cc_start: 0.6809 (pp) cc_final: 0.6229 (tt) REVERT: R 191 PHE cc_start: 0.6667 (t80) cc_final: 0.6446 (t80) REVERT: R 205 MET cc_start: 0.8281 (tpp) cc_final: 0.7690 (tpp) REVERT: R 268 MET cc_start: 0.7471 (tmm) cc_final: 0.7090 (tmm) REVERT: S 222 GLU cc_start: 0.7349 (mm-30) cc_final: 0.6955 (mm-30) outliers start: 52 outliers final: 42 residues processed: 303 average time/residue: 0.2485 time to fit residues: 98.3602 Evaluate side-chains 325 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 276 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 212 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 95 LEU 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 159 THR Chi-restraints excluded: chain B residue 210 LEU 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 18 GLN 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 99 LEU Chi-restraints excluded: chain R residue 118 ILE Chi-restraints excluded: chain R residue 120 LEU 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 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 129 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 77 optimal weight: 0.0770 chunk 5 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.158644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.134939 restraints weight = 14264.315| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.60 r_work: 0.3574 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9177 Z= 0.224 Angle : 0.634 11.086 12421 Z= 0.320 Chirality : 0.043 0.206 1416 Planarity : 0.004 0.065 1547 Dihedral : 5.433 88.064 1290 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 5.18 % Allowed : 27.03 % Favored : 67.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.26), residues: 1118 helix: 2.49 (0.25), residues: 424 sheet: -0.95 (0.29), residues: 290 loop : -0.56 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.004 0.001 HIS R 208 PHE 0.017 0.001 PHE R 106 TYR 0.034 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: 2559.47 seconds wall clock time: 46 minutes 9.28 seconds (2769.28 seconds total)