Starting phenix.real_space_refine on Thu Feb 13 22:19:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6omm_20126/02_2025/6omm_20126.cif Found real_map, /net/cci-nas-00/data/ceres_data/6omm_20126/02_2025/6omm_20126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6omm_20126/02_2025/6omm_20126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6omm_20126/02_2025/6omm_20126.map" model { file = "/net/cci-nas-00/data/ceres_data/6omm_20126/02_2025/6omm_20126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6omm_20126/02_2025/6omm_20126.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 65 5.16 5 C 5907 2.51 5 N 1510 2.21 5 O 1652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9134 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2341 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 13, 'TRANS': 283} Chain: "L" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 59 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "A" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1754 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "C" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "E" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1784 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 194 Unusual residues: {'CLR': 5, 'PLM': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 5.77, per 1000 atoms: 0.63 Number of scatterers: 9134 At special positions: 0 Unit cell: (122.451, 89.523, 128.625, 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 65 16.00 O 1652 8.00 N 1510 7.00 C 5907 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 176 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 991.7 milliseconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB QXV L 9 " Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 38.7% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'R' and resid 21 through 50 Proline residue: R 29 - end of helix removed outlier: 3.665A pdb=" N VAL R 35 " --> pdb=" O VAL R 31 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU R 42 " --> pdb=" O VAL R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 77 removed outlier: 3.705A pdb=" N SER R 73 " --> pdb=" O LEU R 69 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE R 74 " --> pdb=" O ALA R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 88 removed outlier: 3.943A pdb=" N LEU R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 129 removed outlier: 3.702A pdb=" N LYS R 99 " --> pdb=" O TRP R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 136 Processing helix chain 'R' and resid 138 through 146 Processing helix chain 'R' and resid 146 through 157 removed outlier: 4.231A pdb=" N TRP R 150 " --> pdb=" O ILE R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 157 through 164 removed outlier: 4.242A pdb=" N LEU R 162 " --> pdb=" O LEU R 158 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 185 Processing helix chain 'R' and resid 186 through 210 removed outlier: 4.237A pdb=" N LYS R 192 " --> pdb=" O GLU R 188 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL R 193 " --> pdb=" O GLU R 189 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR R 199 " --> pdb=" O ILE R 195 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE R 208 " --> pdb=" O ILE R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 231 removed outlier: 3.712A pdb=" N SER R 215 " --> pdb=" O SER R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 267 removed outlier: 3.707A pdb=" N VAL R 247 " --> pdb=" O LEU R 243 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE R 252 " --> pdb=" O ALA R 248 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS R 253 " --> pdb=" O SER R 249 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TRP R 254 " --> pdb=" O PHE R 250 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE R 255 " --> pdb=" O PHE R 251 " (cutoff:3.500A) Proline residue: R 256 - end of helix removed outlier: 3.595A pdb=" N VAL R 260 " --> pdb=" O PRO R 256 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 273 Processing helix chain 'R' and resid 278 through 303 removed outlier: 3.646A pdb=" N ILE R 282 " --> pdb=" O LYS R 278 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL R 284 " --> pdb=" O ILE R 280 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ASN R 285 " --> pdb=" O ASP R 281 " (cutoff:3.500A) Proline residue: R 286 - end of helix removed outlier: 3.583A pdb=" N ASN R 294 " --> pdb=" O LEU R 290 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER R 295 " --> pdb=" O ALA R 291 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 306 through 317 Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.741A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 51 removed outlier: 3.705A pdb=" N LYS A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 213 removed outlier: 4.144A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.072A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.521A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 352 removed outlier: 4.147A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.993A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.647A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'R' and resid 167 through 168 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 7.108A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.526A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.528A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.157A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.979A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.897A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.907A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.536A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.563A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.048A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN E 194 " --> pdb=" O TYR E 190 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.66 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2798 1.34 - 1.46: 2015 1.46 - 1.58: 4429 1.58 - 1.70: 1 1.70 - 1.82: 96 Bond restraints: 9339 Sorted by residual: bond pdb=" C QXV L 9 " pdb=" NXT QXV L 9 " ideal model delta sigma weight residual 1.339 1.444 -0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" CG LEU B 336 " pdb=" CD2 LEU B 336 " ideal model delta sigma weight residual 1.521 1.416 0.105 3.30e-02 9.18e+02 1.00e+01 bond pdb=" CG LEU B 70 " pdb=" CD2 LEU B 70 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.68e+00 bond pdb=" CG LEU B 336 " pdb=" CD1 LEU B 336 " ideal model delta sigma weight residual 1.521 1.439 0.082 3.30e-02 9.18e+02 6.19e+00 bond pdb=" C LEU R 162 " pdb=" N PHE R 163 " ideal model delta sigma weight residual 1.334 1.369 -0.034 1.43e-02 4.89e+03 5.77e+00 ... (remaining 9334 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 11967 1.84 - 3.68: 566 3.68 - 5.52: 91 5.52 - 7.37: 30 7.37 - 9.21: 8 Bond angle restraints: 12662 Sorted by residual: angle pdb=" N VAL R 160 " pdb=" CA VAL R 160 " pdb=" C VAL R 160 " ideal model delta sigma weight residual 110.72 116.43 -5.71 1.01e+00 9.80e-01 3.20e+01 angle pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta sigma weight residual 121.54 130.75 -9.21 1.91e+00 2.74e-01 2.32e+01 angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 129.67 -8.13 1.91e+00 2.74e-01 1.81e+01 angle pdb=" C ALA B 257 " pdb=" N ASP B 258 " pdb=" CA ASP B 258 " ideal model delta sigma weight residual 122.35 127.61 -5.26 1.46e+00 4.69e-01 1.30e+01 angle pdb=" CA ASN B 119 " pdb=" CB ASN B 119 " pdb=" CG ASN B 119 " ideal model delta sigma weight residual 112.60 116.08 -3.48 1.00e+00 1.00e+00 1.21e+01 ... (remaining 12657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.10: 5426 15.10 - 30.20: 247 30.20 - 45.30: 80 45.30 - 60.40: 1 60.40 - 75.50: 4 Dihedral angle restraints: 5758 sinusoidal: 2468 harmonic: 3290 Sorted by residual: dihedral pdb=" CB CYS R 98 " pdb=" SG CYS R 98 " pdb=" SG CYS R 176 " pdb=" CB CYS R 176 " ideal model delta sinusoidal sigma weight residual -86.00 -121.33 35.33 1 1.00e+01 1.00e-02 1.77e+01 dihedral pdb=" CA HIS E 35 " pdb=" C HIS E 35 " pdb=" N TRP E 36 " pdb=" CA TRP E 36 " ideal model delta harmonic sigma weight residual 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 5755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1298 0.096 - 0.192: 135 0.192 - 0.288: 7 0.288 - 0.384: 6 0.384 - 0.480: 4 Chirality restraints: 1450 Sorted by residual: chirality pdb=" C14 CLR R 403 " pdb=" C13 CLR R 403 " pdb=" C15 CLR R 403 " pdb=" C8 CLR R 403 " both_signs ideal model delta sigma weight residual False -2.32 -2.80 0.48 2.00e-01 2.50e+01 5.77e+00 chirality pdb=" C14 CLR R 404 " pdb=" C13 CLR R 404 " pdb=" C15 CLR R 404 " pdb=" C8 CLR R 404 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.43 2.00e-01 2.50e+01 4.56e+00 chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.39e+00 ... (remaining 1447 not shown) Planarity restraints: 1555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 158 " 0.016 2.00e-02 2.50e+03 3.03e-02 9.16e+00 pdb=" C LEU R 158 " -0.052 2.00e-02 2.50e+03 pdb=" O LEU R 158 " 0.019 2.00e-02 2.50e+03 pdb=" N PRO R 159 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 111 " 0.018 2.00e-02 2.50e+03 1.69e-02 7.11e+00 pdb=" CG TRP E 111 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP E 111 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP E 111 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 111 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 111 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 111 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 111 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 111 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP E 111 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 27 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.03e+00 pdb=" C ILE R 27 " -0.039 2.00e-02 2.50e+03 pdb=" O ILE R 27 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU R 28 " 0.013 2.00e-02 2.50e+03 ... (remaining 1552 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 911 2.76 - 3.29: 8556 3.29 - 3.83: 15205 3.83 - 4.36: 17772 4.36 - 4.90: 31044 Nonbonded interactions: 73488 Sorted by model distance: nonbonded pdb=" O ALA R 153 " pdb=" OG1 THR R 157 " model vdw 2.222 3.040 nonbonded pdb=" OG SER B 281 " pdb=" O HIS C 44 " model vdw 2.279 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.300 3.040 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.352 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.357 3.040 ... (remaining 73483 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: 1.080 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.400 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 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 : 0.005 0.105 9339 Z= 0.328 Angle : 0.928 9.207 12662 Z= 0.483 Chirality : 0.064 0.480 1450 Planarity : 0.006 0.048 1555 Dihedral : 9.848 75.504 3629 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -2.94 (0.21), residues: 1123 helix: -1.84 (0.20), residues: 410 sheet: -1.61 (0.29), residues: 273 loop : -2.06 (0.25), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP E 111 HIS 0.008 0.002 HIS E 35 PHE 0.033 0.003 PHE R 161 TYR 0.021 0.002 TYR E 59 ARG 0.015 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 39 LEU cc_start: 0.8789 (tt) cc_final: 0.8500 (tt) REVERT: R 90 LYS cc_start: 0.7884 (mttt) cc_final: 0.6884 (mmmt) REVERT: R 174 THR cc_start: 0.6256 (p) cc_final: 0.5610 (p) REVERT: R 179 ASN cc_start: 0.7691 (t0) cc_final: 0.7161 (m110) REVERT: R 191 LEU cc_start: 0.6671 (tp) cc_final: 0.6432 (pp) REVERT: R 300 MET cc_start: 0.8486 (mtt) cc_final: 0.8215 (mtm) REVERT: A 48 THR cc_start: 0.8560 (m) cc_final: 0.8289 (p) REVERT: A 327 THR cc_start: 0.8168 (p) cc_final: 0.7403 (m) REVERT: A 346 ASN cc_start: 0.8778 (m-40) cc_final: 0.8513 (m110) REVERT: B 267 ASP cc_start: 0.8710 (m-30) cc_final: 0.8263 (t0) REVERT: B 273 ILE cc_start: 0.8378 (mp) cc_final: 0.8163 (mt) REVERT: B 291 ASP cc_start: 0.7792 (t70) cc_final: 0.7490 (t70) REVERT: B 297 TRP cc_start: 0.8763 (m100) cc_final: 0.8362 (m100) REVERT: E 217 SER cc_start: 0.8144 (t) cc_final: 0.6768 (p) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.2669 time to fit residues: 113.6328 Evaluate side-chains 203 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 307 GLN A 204 GLN B 32 GLN B 62 HIS B 91 HIS B 175 GLN E 13 GLN E 142 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.141925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.105061 restraints weight = 13387.975| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.38 r_work: 0.3176 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 9339 Z= 0.267 Angle : 0.622 8.237 12662 Z= 0.321 Chirality : 0.043 0.150 1450 Planarity : 0.004 0.036 1555 Dihedral : 6.130 56.219 1596 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.87 % Allowed : 11.99 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.23), residues: 1123 helix: 0.11 (0.25), residues: 417 sheet: -1.21 (0.29), residues: 268 loop : -1.59 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 169 HIS 0.006 0.001 HIS B 91 PHE 0.017 0.001 PHE R 96 TYR 0.016 0.002 TYR B 59 ARG 0.006 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 213 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 71 ASP cc_start: 0.7855 (t70) cc_final: 0.7502 (t70) REVERT: R 90 LYS cc_start: 0.8221 (mttt) cc_final: 0.7932 (mmmm) REVERT: R 191 LEU cc_start: 0.7024 (tp) cc_final: 0.6573 (pp) REVERT: R 270 GLU cc_start: 0.7610 (mp0) cc_final: 0.7396 (tp30) REVERT: R 300 MET cc_start: 0.8519 (mtt) cc_final: 0.8216 (mtm) REVERT: L 7 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6979 (mtp) REVERT: A 48 THR cc_start: 0.8337 (m) cc_final: 0.8062 (p) REVERT: A 52 GLN cc_start: 0.7003 (OUTLIER) cc_final: 0.6454 (tt0) REVERT: A 315 ASP cc_start: 0.7382 (p0) cc_final: 0.7080 (p0) REVERT: A 327 THR cc_start: 0.7997 (p) cc_final: 0.7650 (m) REVERT: A 331 ASN cc_start: 0.8011 (m-40) cc_final: 0.7740 (m110) REVERT: A 346 ASN cc_start: 0.8954 (m-40) cc_final: 0.8651 (m110) REVERT: B 12 GLU cc_start: 0.8591 (tp30) cc_final: 0.8340 (mt-10) REVERT: B 101 MET cc_start: 0.8855 (mmm) cc_final: 0.8542 (mmm) REVERT: B 267 ASP cc_start: 0.8437 (m-30) cc_final: 0.8021 (t0) REVERT: B 273 ILE cc_start: 0.9112 (mp) cc_final: 0.8910 (mt) REVERT: B 291 ASP cc_start: 0.7945 (t70) cc_final: 0.7452 (t70) REVERT: B 297 TRP cc_start: 0.9122 (m100) cc_final: 0.8636 (m100) REVERT: B 304 ARG cc_start: 0.8454 (ttp-170) cc_final: 0.8230 (ttp-170) REVERT: E 6 GLU cc_start: 0.8217 (mp0) cc_final: 0.7726 (mp0) REVERT: E 153 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8164 (pt0) REVERT: E 220 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7359 (mp0) outliers start: 28 outliers final: 12 residues processed: 230 average time/residue: 0.2445 time to fit residues: 75.4566 Evaluate side-chains 200 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 157 THR Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain L residue 7 MET Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 139 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 80 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 83 optimal weight: 20.0000 chunk 72 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 87 optimal weight: 0.0170 overall best weight: 1.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 44 ASN R 66 ASN ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN A 333 GLN B 175 GLN C 58 GLN E 13 GLN E 77 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.139564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.106288 restraints weight = 13755.909| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.66 r_work: 0.3117 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 9339 Z= 0.272 Angle : 0.597 9.115 12662 Z= 0.306 Chirality : 0.042 0.194 1450 Planarity : 0.004 0.043 1555 Dihedral : 5.924 56.701 1596 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.69 % Allowed : 13.42 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.24), residues: 1123 helix: 0.77 (0.26), residues: 415 sheet: -0.95 (0.29), residues: 260 loop : -1.36 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 211 HIS 0.005 0.001 HIS B 142 PHE 0.012 0.001 PHE B 234 TYR 0.015 0.001 TYR B 59 ARG 0.006 0.001 ARG E 218 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 196 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 72 PHE cc_start: 0.8292 (t80) cc_final: 0.8057 (t80) REVERT: R 90 LYS cc_start: 0.8317 (mttt) cc_final: 0.8049 (mmmm) REVERT: R 161 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7528 (t80) REVERT: R 191 LEU cc_start: 0.7072 (tp) cc_final: 0.6625 (pp) REVERT: R 300 MET cc_start: 0.8532 (mtt) cc_final: 0.8166 (mtm) REVERT: A 48 THR cc_start: 0.8357 (m) cc_final: 0.8122 (p) REVERT: A 52 GLN cc_start: 0.6948 (OUTLIER) cc_final: 0.6573 (tt0) REVERT: A 242 ARG cc_start: 0.7689 (mtt-85) cc_final: 0.7371 (mtt-85) REVERT: A 327 THR cc_start: 0.8059 (p) cc_final: 0.7801 (m) REVERT: A 331 ASN cc_start: 0.7965 (m-40) cc_final: 0.7613 (m110) REVERT: B 12 GLU cc_start: 0.8624 (tp30) cc_final: 0.8391 (mt-10) REVERT: B 267 ASP cc_start: 0.8260 (m-30) cc_final: 0.7951 (t0) REVERT: B 291 ASP cc_start: 0.7811 (t70) cc_final: 0.7325 (t70) REVERT: B 297 TRP cc_start: 0.9107 (m100) cc_final: 0.8589 (m100) REVERT: B 304 ARG cc_start: 0.8199 (ttp-170) cc_final: 0.7957 (ttp-170) REVERT: C 9 ILE cc_start: 0.4738 (OUTLIER) cc_final: 0.4415 (mp) REVERT: E 6 GLU cc_start: 0.8170 (mp0) cc_final: 0.7870 (mp0) REVERT: E 219 LEU cc_start: 0.8735 (mt) cc_final: 0.8445 (mp) outliers start: 36 outliers final: 22 residues processed: 219 average time/residue: 0.2432 time to fit residues: 71.1814 Evaluate side-chains 213 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 308 ASP Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 141 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 41 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 81 optimal weight: 0.1980 chunk 104 optimal weight: 0.0970 chunk 17 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN E 13 GLN E 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.142154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.109523 restraints weight = 13535.504| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.54 r_work: 0.3173 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 9339 Z= 0.181 Angle : 0.569 8.830 12662 Z= 0.289 Chirality : 0.040 0.169 1450 Planarity : 0.003 0.045 1555 Dihedral : 5.548 58.330 1596 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.38 % Allowed : 14.14 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.39 (0.25), residues: 1123 helix: 1.12 (0.26), residues: 416 sheet: -0.62 (0.31), residues: 252 loop : -1.30 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS R 102 PHE 0.009 0.001 PHE E 32 TYR 0.011 0.001 TYR B 59 ARG 0.004 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 90 LYS cc_start: 0.8303 (mttt) cc_final: 0.8003 (mmmm) REVERT: R 161 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7607 (t80) REVERT: R 191 LEU cc_start: 0.7036 (tp) cc_final: 0.6617 (pp) REVERT: A 48 THR cc_start: 0.8328 (m) cc_final: 0.8085 (p) REVERT: A 52 GLN cc_start: 0.6817 (OUTLIER) cc_final: 0.6415 (tt0) REVERT: A 242 ARG cc_start: 0.7715 (mtt-85) cc_final: 0.7355 (mtt-85) REVERT: A 306 GLN cc_start: 0.8241 (tp40) cc_final: 0.7956 (tp40) REVERT: A 327 THR cc_start: 0.7927 (p) cc_final: 0.7558 (m) REVERT: A 331 ASN cc_start: 0.7906 (m-40) cc_final: 0.7606 (m110) REVERT: B 12 GLU cc_start: 0.8611 (tp30) cc_final: 0.8391 (mt-10) REVERT: B 207 SER cc_start: 0.8729 (m) cc_final: 0.8429 (p) REVERT: B 219 ARG cc_start: 0.8808 (mmm-85) cc_final: 0.8496 (mtt-85) REVERT: B 267 ASP cc_start: 0.8195 (m-30) cc_final: 0.7860 (t0) REVERT: B 291 ASP cc_start: 0.7637 (t70) cc_final: 0.7130 (t70) REVERT: B 297 TRP cc_start: 0.9031 (m100) cc_final: 0.8535 (m100) REVERT: B 331 SER cc_start: 0.8791 (OUTLIER) cc_final: 0.8569 (t) REVERT: E 161 SER cc_start: 0.8907 (t) cc_final: 0.8444 (t) REVERT: E 218 ARG cc_start: 0.6668 (mmp-170) cc_final: 0.6305 (mmp-170) outliers start: 33 outliers final: 19 residues processed: 215 average time/residue: 0.2504 time to fit residues: 72.6552 Evaluate side-chains 201 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 139 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 4 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN E 13 GLN E 77 ASN E 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.139013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.106232 restraints weight = 13506.005| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.62 r_work: 0.3107 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 9339 Z= 0.257 Angle : 0.604 9.305 12662 Z= 0.305 Chirality : 0.042 0.156 1450 Planarity : 0.004 0.048 1555 Dihedral : 5.536 55.910 1596 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.10 % Allowed : 14.65 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.28 (0.25), residues: 1123 helix: 1.23 (0.26), residues: 419 sheet: -0.57 (0.31), residues: 253 loop : -1.26 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS R 102 PHE 0.009 0.001 PHE E 27 TYR 0.015 0.001 TYR B 59 ARG 0.005 0.000 ARG R 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 161 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7726 (t80) REVERT: R 191 LEU cc_start: 0.6835 (tp) cc_final: 0.6543 (pp) REVERT: A 48 THR cc_start: 0.8304 (m) cc_final: 0.8016 (p) REVERT: A 52 GLN cc_start: 0.6855 (OUTLIER) cc_final: 0.6582 (tt0) REVERT: A 242 ARG cc_start: 0.7826 (mtt-85) cc_final: 0.7404 (mtt-85) REVERT: A 306 GLN cc_start: 0.8302 (tp40) cc_final: 0.7984 (tp40) REVERT: A 327 THR cc_start: 0.7880 (p) cc_final: 0.7604 (m) REVERT: A 331 ASN cc_start: 0.8060 (m-40) cc_final: 0.7712 (m110) REVERT: B 12 GLU cc_start: 0.8594 (tp30) cc_final: 0.8335 (mt-10) REVERT: B 243 THR cc_start: 0.8898 (m) cc_final: 0.8223 (p) REVERT: B 267 ASP cc_start: 0.8305 (m-30) cc_final: 0.7968 (t0) REVERT: B 291 ASP cc_start: 0.7821 (t70) cc_final: 0.7326 (t70) REVERT: B 297 TRP cc_start: 0.9125 (m100) cc_final: 0.8612 (m100) REVERT: B 331 SER cc_start: 0.8872 (OUTLIER) cc_final: 0.8654 (t) REVERT: E 89 GLU cc_start: 0.7527 (tp30) cc_final: 0.7228 (tp30) REVERT: E 140 MET cc_start: 0.8633 (mmm) cc_final: 0.7713 (mmm) REVERT: E 161 SER cc_start: 0.8902 (t) cc_final: 0.8307 (t) REVERT: E 218 ARG cc_start: 0.6572 (mmp-170) cc_final: 0.6304 (mmm160) REVERT: E 220 GLU cc_start: 0.7137 (mp0) cc_final: 0.6321 (mp0) outliers start: 40 outliers final: 25 residues processed: 211 average time/residue: 0.2389 time to fit residues: 68.3895 Evaluate side-chains 200 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 139 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 16 optimal weight: 3.9990 chunk 35 optimal weight: 0.0980 chunk 47 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 34 optimal weight: 0.0980 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 0.0980 chunk 63 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 overall best weight: 0.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN E 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.143706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.111859 restraints weight = 13425.559| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.51 r_work: 0.3205 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 9339 Z= 0.160 Angle : 0.561 8.431 12662 Z= 0.285 Chirality : 0.040 0.145 1450 Planarity : 0.003 0.047 1555 Dihedral : 5.088 54.874 1596 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.28 % Allowed : 15.88 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.25), residues: 1123 helix: 1.40 (0.26), residues: 421 sheet: -0.43 (0.31), residues: 266 loop : -1.20 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS R 102 PHE 0.010 0.001 PHE E 32 TYR 0.011 0.001 TYR E 190 ARG 0.007 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: R 26 ARG cc_start: 0.7406 (ttp-110) cc_final: 0.7098 (mtp85) REVERT: R 157 THR cc_start: 0.8067 (m) cc_final: 0.7757 (t) REVERT: R 161 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7774 (t80) REVERT: R 179 ASN cc_start: 0.8041 (t0) cc_final: 0.6798 (m110) REVERT: R 190 ARG cc_start: 0.6720 (ptm-80) cc_final: 0.6352 (ptm-80) REVERT: L 8 VAL cc_start: 0.7902 (OUTLIER) cc_final: 0.7669 (p) REVERT: A 48 THR cc_start: 0.8182 (m) cc_final: 0.7898 (p) REVERT: A 52 GLN cc_start: 0.6854 (OUTLIER) cc_final: 0.6609 (tt0) REVERT: A 242 ARG cc_start: 0.7779 (mtt-85) cc_final: 0.7391 (mtt-85) REVERT: A 306 GLN cc_start: 0.8288 (tp40) cc_final: 0.8062 (tp40) REVERT: A 331 ASN cc_start: 0.7942 (m-40) cc_final: 0.7655 (m110) REVERT: B 12 GLU cc_start: 0.8629 (tp30) cc_final: 0.8356 (mt-10) REVERT: B 172 GLU cc_start: 0.7690 (pm20) cc_final: 0.6763 (pm20) REVERT: B 207 SER cc_start: 0.8704 (m) cc_final: 0.8425 (p) REVERT: B 234 PHE cc_start: 0.9376 (OUTLIER) cc_final: 0.9013 (m-80) REVERT: B 267 ASP cc_start: 0.8183 (m-30) cc_final: 0.7844 (t0) REVERT: B 291 ASP cc_start: 0.7440 (t70) cc_final: 0.7002 (t70) REVERT: B 297 TRP cc_start: 0.8905 (m100) cc_final: 0.8545 (m100) REVERT: B 331 SER cc_start: 0.8787 (t) cc_final: 0.8563 (t) REVERT: E 140 MET cc_start: 0.8610 (mmm) cc_final: 0.7586 (mmm) REVERT: E 161 SER cc_start: 0.8807 (t) cc_final: 0.8456 (p) REVERT: E 218 ARG cc_start: 0.6596 (mmp-170) cc_final: 0.6315 (mmm160) REVERT: E 220 GLU cc_start: 0.7149 (mp0) cc_final: 0.6347 (mp0) outliers start: 32 outliers final: 20 residues processed: 216 average time/residue: 0.2364 time to fit residues: 70.1109 Evaluate side-chains 203 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 179 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 139 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 84 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 34 optimal weight: 0.4980 chunk 56 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN E 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.143733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.108603 restraints weight = 13486.408| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.39 r_work: 0.3198 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9339 Z= 0.198 Angle : 0.572 7.183 12662 Z= 0.294 Chirality : 0.040 0.157 1450 Planarity : 0.003 0.048 1555 Dihedral : 5.000 56.986 1596 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.89 % Allowed : 16.80 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.05 (0.25), residues: 1123 helix: 1.50 (0.27), residues: 421 sheet: -0.36 (0.30), residues: 275 loop : -1.14 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 91 HIS 0.004 0.001 HIS R 102 PHE 0.010 0.001 PHE E 32 TYR 0.012 0.001 TYR E 103 ARG 0.007 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: R 26 ARG cc_start: 0.7385 (ttp-110) cc_final: 0.7151 (ptp-110) REVERT: R 157 THR cc_start: 0.8150 (m) cc_final: 0.7811 (t) REVERT: R 161 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.7946 (t80) REVERT: R 179 ASN cc_start: 0.8149 (t0) cc_final: 0.6810 (m110) REVERT: R 190 ARG cc_start: 0.6766 (ptm-80) cc_final: 0.6393 (ptm-80) REVERT: A 48 THR cc_start: 0.8289 (m) cc_final: 0.7932 (p) REVERT: A 242 ARG cc_start: 0.7904 (mtt-85) cc_final: 0.7703 (mtt-85) REVERT: A 306 GLN cc_start: 0.8386 (tp40) cc_final: 0.8143 (tp40) REVERT: A 331 ASN cc_start: 0.8163 (m-40) cc_final: 0.7751 (m110) REVERT: B 12 GLU cc_start: 0.8640 (tp30) cc_final: 0.8286 (mt-10) REVERT: B 207 SER cc_start: 0.8826 (m) cc_final: 0.8611 (p) REVERT: B 234 PHE cc_start: 0.9458 (OUTLIER) cc_final: 0.9102 (m-80) REVERT: B 267 ASP cc_start: 0.8477 (m-30) cc_final: 0.8062 (t0) REVERT: B 291 ASP cc_start: 0.7817 (t70) cc_final: 0.7374 (t70) REVERT: B 297 TRP cc_start: 0.9052 (m100) cc_final: 0.8709 (m100) REVERT: B 331 SER cc_start: 0.8985 (OUTLIER) cc_final: 0.8783 (t) REVERT: E 89 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7466 (tp30) REVERT: E 153 GLU cc_start: 0.8350 (pt0) cc_final: 0.7884 (pm20) REVERT: E 161 SER cc_start: 0.9010 (t) cc_final: 0.8744 (p) outliers start: 38 outliers final: 22 residues processed: 203 average time/residue: 0.2214 time to fit residues: 61.6106 Evaluate side-chains 200 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 139 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 86 optimal weight: 0.2980 chunk 75 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 48 optimal weight: 0.0870 chunk 63 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 0.0570 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN E 13 GLN E 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.144817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.107917 restraints weight = 13427.410| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.35 r_work: 0.3224 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 9339 Z= 0.187 Angle : 0.581 7.289 12662 Z= 0.297 Chirality : 0.040 0.155 1450 Planarity : 0.003 0.048 1555 Dihedral : 4.816 56.425 1596 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.07 % Allowed : 17.21 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.07 (0.25), residues: 1123 helix: 1.44 (0.26), residues: 424 sheet: -0.22 (0.31), residues: 269 loop : -1.15 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS R 102 PHE 0.010 0.001 PHE E 32 TYR 0.016 0.001 TYR B 264 ARG 0.007 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 26 ARG cc_start: 0.7313 (ttp-110) cc_final: 0.7083 (ptp-110) REVERT: R 157 THR cc_start: 0.8188 (m) cc_final: 0.7865 (t) REVERT: R 161 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.7932 (t80) REVERT: R 179 ASN cc_start: 0.8121 (t0) cc_final: 0.6790 (m110) REVERT: R 190 ARG cc_start: 0.6791 (ptm-80) cc_final: 0.6441 (ptm-80) REVERT: R 295 SER cc_start: 0.8778 (OUTLIER) cc_final: 0.8436 (t) REVERT: R 298 ASN cc_start: 0.8569 (m-40) cc_final: 0.8296 (m-40) REVERT: A 48 THR cc_start: 0.8140 (m) cc_final: 0.7839 (p) REVERT: A 242 ARG cc_start: 0.7871 (mtt-85) cc_final: 0.7669 (mtt-85) REVERT: A 306 GLN cc_start: 0.8356 (tp40) cc_final: 0.8126 (tp40) REVERT: A 331 ASN cc_start: 0.8013 (m-40) cc_final: 0.7689 (m110) REVERT: B 12 GLU cc_start: 0.8722 (tp30) cc_final: 0.8416 (mt-10) REVERT: B 15 LYS cc_start: 0.8330 (mtmm) cc_final: 0.7837 (mtmm) REVERT: B 207 SER cc_start: 0.8815 (m) cc_final: 0.8593 (p) REVERT: B 217 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.7019 (ppp) REVERT: B 234 PHE cc_start: 0.9445 (OUTLIER) cc_final: 0.9057 (m-80) REVERT: B 243 THR cc_start: 0.8950 (m) cc_final: 0.8454 (p) REVERT: B 267 ASP cc_start: 0.8449 (m-30) cc_final: 0.7979 (t0) REVERT: B 273 ILE cc_start: 0.9161 (mp) cc_final: 0.8868 (mt) REVERT: B 291 ASP cc_start: 0.7742 (t70) cc_final: 0.7301 (t70) REVERT: B 297 TRP cc_start: 0.9003 (m100) cc_final: 0.8644 (m100) REVERT: B 331 SER cc_start: 0.8898 (t) cc_final: 0.8694 (t) REVERT: E 140 MET cc_start: 0.8759 (mmm) cc_final: 0.7727 (mmm) REVERT: E 153 GLU cc_start: 0.8321 (pt0) cc_final: 0.7886 (pm20) REVERT: E 161 SER cc_start: 0.8980 (t) cc_final: 0.8615 (p) outliers start: 30 outliers final: 22 residues processed: 212 average time/residue: 0.2130 time to fit residues: 62.7342 Evaluate side-chains 207 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 295 SER Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 109 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 86 optimal weight: 7.9990 chunk 106 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 50 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 ASN ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.137945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.105233 restraints weight = 13506.015| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.62 r_work: 0.3089 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 9339 Z= 0.303 Angle : 0.634 7.239 12662 Z= 0.325 Chirality : 0.043 0.155 1450 Planarity : 0.004 0.049 1555 Dihedral : 5.176 56.986 1596 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.18 % Allowed : 17.52 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.10 (0.25), residues: 1123 helix: 1.47 (0.26), residues: 420 sheet: -0.35 (0.31), residues: 262 loop : -0.99 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP R 91 HIS 0.007 0.001 HIS R 102 PHE 0.010 0.001 PHE E 27 TYR 0.011 0.002 TYR E 190 ARG 0.006 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: R 26 ARG cc_start: 0.7451 (ttp-110) cc_final: 0.7215 (ptp-110) REVERT: R 157 THR cc_start: 0.8112 (m) cc_final: 0.7796 (t) REVERT: R 161 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.8028 (t80) REVERT: R 179 ASN cc_start: 0.8175 (t0) cc_final: 0.6845 (m110) REVERT: R 295 SER cc_start: 0.8658 (OUTLIER) cc_final: 0.8319 (t) REVERT: A 48 THR cc_start: 0.8124 (m) cc_final: 0.7807 (p) REVERT: A 53 MET cc_start: 0.6390 (mmt) cc_final: 0.5930 (mmt) REVERT: A 242 ARG cc_start: 0.7917 (mtt-85) cc_final: 0.7685 (mtt-85) REVERT: A 306 GLN cc_start: 0.8288 (tp40) cc_final: 0.8033 (tp40) REVERT: B 10 GLU cc_start: 0.7976 (tp30) cc_final: 0.7755 (tp30) REVERT: B 12 GLU cc_start: 0.8643 (tp30) cc_final: 0.8417 (mt-10) REVERT: B 15 LYS cc_start: 0.8404 (mtmm) cc_final: 0.7903 (mtmm) REVERT: B 207 SER cc_start: 0.8845 (m) cc_final: 0.8546 (p) REVERT: B 217 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.6959 (ppp) REVERT: B 234 PHE cc_start: 0.9475 (OUTLIER) cc_final: 0.8966 (m-80) REVERT: B 243 THR cc_start: 0.8920 (m) cc_final: 0.8374 (p) REVERT: B 267 ASP cc_start: 0.8210 (m-30) cc_final: 0.7872 (t0) REVERT: B 291 ASP cc_start: 0.7742 (t70) cc_final: 0.7334 (t70) REVERT: B 297 TRP cc_start: 0.9129 (m100) cc_final: 0.8741 (m100) REVERT: B 331 SER cc_start: 0.8815 (OUTLIER) cc_final: 0.8584 (t) REVERT: E 140 MET cc_start: 0.8700 (mmm) cc_final: 0.7840 (mmm) REVERT: E 153 GLU cc_start: 0.8263 (pt0) cc_final: 0.8026 (pt0) REVERT: E 161 SER cc_start: 0.8994 (t) cc_final: 0.8720 (p) outliers start: 31 outliers final: 23 residues processed: 201 average time/residue: 0.2157 time to fit residues: 60.5247 Evaluate side-chains 200 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 295 SER Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 109 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 104 optimal weight: 0.3980 chunk 97 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.140733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.106339 restraints weight = 13381.160| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.24 r_work: 0.3165 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 9339 Z= 0.216 Angle : 0.603 8.128 12662 Z= 0.309 Chirality : 0.041 0.152 1450 Planarity : 0.004 0.049 1555 Dihedral : 4.921 55.715 1596 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.87 % Allowed : 17.42 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.10 (0.25), residues: 1123 helix: 1.43 (0.26), residues: 423 sheet: -0.30 (0.31), residues: 279 loop : -1.01 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 91 HIS 0.005 0.001 HIS R 102 PHE 0.009 0.001 PHE E 80 TYR 0.011 0.001 TYR E 190 ARG 0.006 0.000 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 26 ARG cc_start: 0.7485 (ttp-110) cc_final: 0.7240 (ptp-110) REVERT: R 157 THR cc_start: 0.8198 (m) cc_final: 0.7867 (t) REVERT: R 161 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.8014 (t80) REVERT: R 179 ASN cc_start: 0.8152 (t0) cc_final: 0.6729 (m110) REVERT: R 295 SER cc_start: 0.8840 (OUTLIER) cc_final: 0.8493 (t) REVERT: A 48 THR cc_start: 0.8116 (m) cc_final: 0.7797 (p) REVERT: A 242 ARG cc_start: 0.7969 (mtt-85) cc_final: 0.7742 (mtt-85) REVERT: B 12 GLU cc_start: 0.8727 (tp30) cc_final: 0.8423 (mt-10) REVERT: B 15 LYS cc_start: 0.8349 (mtmm) cc_final: 0.7857 (mtmm) REVERT: B 207 SER cc_start: 0.8902 (m) cc_final: 0.8627 (p) REVERT: B 217 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.7189 (ppp) REVERT: B 234 PHE cc_start: 0.9504 (OUTLIER) cc_final: 0.9016 (m-80) REVERT: B 243 THR cc_start: 0.8980 (m) cc_final: 0.8477 (p) REVERT: B 267 ASP cc_start: 0.8392 (m-30) cc_final: 0.8086 (m-30) REVERT: B 291 ASP cc_start: 0.7855 (t70) cc_final: 0.7423 (t70) REVERT: B 297 TRP cc_start: 0.9132 (m100) cc_final: 0.8743 (m100) REVERT: B 331 SER cc_start: 0.8939 (t) cc_final: 0.8730 (t) REVERT: E 140 MET cc_start: 0.8805 (mmm) cc_final: 0.7926 (mmm) REVERT: E 161 SER cc_start: 0.9078 (t) cc_final: 0.8758 (p) outliers start: 28 outliers final: 21 residues processed: 197 average time/residue: 0.2140 time to fit residues: 58.6258 Evaluate side-chains 192 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 295 SER Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 109 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 66 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 57 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN E 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.135306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.097762 restraints weight = 13543.604| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.33 r_work: 0.3064 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 9339 Z= 0.352 Angle : 0.671 8.709 12662 Z= 0.342 Chirality : 0.044 0.161 1450 Planarity : 0.004 0.049 1555 Dihedral : 5.361 57.409 1596 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.38 % Allowed : 17.52 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.04 (0.25), residues: 1123 helix: 1.38 (0.26), residues: 420 sheet: -0.48 (0.30), residues: 275 loop : -0.92 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 91 HIS 0.007 0.001 HIS R 102 PHE 0.010 0.001 PHE E 27 TYR 0.014 0.002 TYR B 59 ARG 0.006 0.001 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5421.02 seconds wall clock time: 96 minutes 54.32 seconds (5814.32 seconds total)