Starting phenix.real_space_refine on Fri Mar 14 02:02:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6omm_20126/03_2025/6omm_20126.cif Found real_map, /net/cci-nas-00/data/ceres_data/6omm_20126/03_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_20126/03_2025/6omm_20126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6omm_20126/03_2025/6omm_20126.map" model { file = "/net/cci-nas-00/data/ceres_data/6omm_20126/03_2025/6omm_20126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6omm_20126/03_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.65, per 1000 atoms: 0.62 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: 2.35 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.09 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: 2.56 Time building geometry restraints manager: 2.70 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: 0.980 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.770 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.340 ------------------------------------------------------------------------------- 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 : 0.948 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: 0.2622 time to fit residues: 111.2380 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 : 1.018 ------------------------------------------------------------------------------- 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 = 51)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.105064 restraints weight = 13387.976| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.38 r_work: 0.3177 rms_B_bonded: 3.04 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 : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 71 ASP cc_start: 0.7854 (t70) cc_final: 0.7497 (t70) REVERT: R 90 LYS cc_start: 0.8221 (mttt) cc_final: 0.7930 (mmmm) REVERT: R 191 LEU cc_start: 0.7021 (tp) cc_final: 0.6564 (pp) REVERT: R 270 GLU cc_start: 0.7605 (mp0) cc_final: 0.7387 (tp30) REVERT: R 300 MET cc_start: 0.8517 (mtt) cc_final: 0.8210 (mtm) REVERT: L 7 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6976 (mtp) REVERT: A 48 THR cc_start: 0.8329 (m) cc_final: 0.8052 (p) REVERT: A 52 GLN cc_start: 0.7004 (OUTLIER) cc_final: 0.6453 (tt0) REVERT: A 315 ASP cc_start: 0.7370 (p0) cc_final: 0.7071 (p0) REVERT: A 327 THR cc_start: 0.7994 (p) cc_final: 0.7649 (m) REVERT: A 331 ASN cc_start: 0.8012 (m-40) cc_final: 0.7740 (m110) REVERT: A 346 ASN cc_start: 0.8954 (m-40) cc_final: 0.8650 (m110) REVERT: B 12 GLU cc_start: 0.8587 (tp30) cc_final: 0.8332 (mt-10) REVERT: B 101 MET cc_start: 0.8853 (mmm) cc_final: 0.8541 (mmm) REVERT: B 267 ASP cc_start: 0.8423 (m-30) cc_final: 0.8014 (t0) REVERT: B 273 ILE cc_start: 0.9113 (mp) cc_final: 0.8910 (mt) REVERT: B 291 ASP cc_start: 0.7948 (t70) cc_final: 0.7456 (t70) REVERT: B 297 TRP cc_start: 0.9122 (m100) cc_final: 0.8635 (m100) REVERT: B 304 ARG cc_start: 0.8455 (ttp-170) cc_final: 0.8231 (ttp-170) REVERT: E 6 GLU cc_start: 0.8217 (mp0) cc_final: 0.7725 (mp0) REVERT: E 153 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8163 (pt0) REVERT: E 220 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7355 (mp0) outliers start: 28 outliers final: 12 residues processed: 230 average time/residue: 0.2329 time to fit residues: 71.3465 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 : 0.956 ------------------------------------------------------------------------------- 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: 5.9990 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 44 ASN R 258 GLN ** R 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 175 GLN C 58 GLN E 13 GLN E 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.138806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.105473 restraints weight = 13756.061| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.68 r_work: 0.3103 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 9339 Z= 0.290 Angle : 0.610 9.193 12662 Z= 0.312 Chirality : 0.043 0.206 1450 Planarity : 0.004 0.044 1555 Dihedral : 5.961 57.641 1596 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.59 % Allowed : 13.32 % Favored : 83.09 % 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: -0.75 (0.24), residues: 1123 helix: 0.76 (0.26), residues: 415 sheet: -0.90 (0.30), residues: 254 loop : -1.36 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.006 0.001 HIS B 142 PHE 0.013 0.001 PHE B 234 TYR 0.016 0.002 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 225 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 190 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 72 PHE cc_start: 0.8314 (t80) cc_final: 0.8044 (t80) REVERT: R 90 LYS cc_start: 0.8320 (mttt) cc_final: 0.8057 (mmmm) REVERT: R 161 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7584 (t80) REVERT: R 191 LEU cc_start: 0.7101 (tp) cc_final: 0.6674 (pp) REVERT: R 300 MET cc_start: 0.8558 (mtt) cc_final: 0.8200 (mtm) REVERT: A 48 THR cc_start: 0.8361 (m) cc_final: 0.8122 (p) REVERT: A 52 GLN cc_start: 0.6950 (OUTLIER) cc_final: 0.6616 (tt0) REVERT: A 242 ARG cc_start: 0.7733 (mtt-85) cc_final: 0.7455 (mtt-85) REVERT: A 327 THR cc_start: 0.8038 (p) cc_final: 0.7822 (m) REVERT: A 331 ASN cc_start: 0.8014 (m-40) cc_final: 0.7655 (m110) REVERT: B 12 GLU cc_start: 0.8570 (tp30) cc_final: 0.8350 (mt-10) REVERT: B 267 ASP cc_start: 0.8287 (m-30) cc_final: 0.7969 (t0) REVERT: B 291 ASP cc_start: 0.7847 (t70) cc_final: 0.7359 (t70) REVERT: E 6 GLU cc_start: 0.8203 (mp0) cc_final: 0.7903 (mp0) REVERT: E 219 LEU cc_start: 0.8705 (mt) cc_final: 0.8398 (mp) outliers start: 35 outliers final: 20 residues processed: 212 average time/residue: 0.2938 time to fit residues: 83.1283 Evaluate side-chains 204 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 70 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 101 optimal weight: 20.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.138444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.105619 restraints weight = 13524.591| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.63 r_work: 0.3099 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 9339 Z= 0.266 Angle : 0.604 8.928 12662 Z= 0.306 Chirality : 0.042 0.166 1450 Planarity : 0.004 0.046 1555 Dihedral : 5.738 59.190 1596 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.41 % Allowed : 14.04 % Favored : 81.56 % 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: -0.46 (0.25), residues: 1123 helix: 1.09 (0.26), residues: 415 sheet: -0.72 (0.30), residues: 252 loop : -1.32 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 95 HIS 0.006 0.001 HIS R 102 PHE 0.010 0.001 PHE E 27 TYR 0.014 0.001 TYR B 59 ARG 0.003 0.000 ARG R 190 *********************** 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 230 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 1.217 Fit side-chains revert: symmetry clash REVERT: R 26 ARG cc_start: 0.7519 (ttp-110) cc_final: 0.7224 (ptp-170) REVERT: R 90 LYS cc_start: 0.8296 (mttt) cc_final: 0.8029 (mmmm) REVERT: R 161 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7673 (t80) REVERT: R 191 LEU cc_start: 0.7101 (tp) cc_final: 0.6673 (pp) REVERT: R 300 MET cc_start: 0.8508 (mtt) cc_final: 0.8146 (mtm) REVERT: A 48 THR cc_start: 0.8378 (m) cc_final: 0.8133 (p) REVERT: A 52 GLN cc_start: 0.6817 (OUTLIER) cc_final: 0.6509 (tt0) REVERT: A 242 ARG cc_start: 0.7860 (mtt-85) cc_final: 0.7441 (mtt-85) REVERT: A 306 GLN cc_start: 0.8277 (tp40) cc_final: 0.7981 (tp40) REVERT: A 327 THR cc_start: 0.7963 (p) cc_final: 0.7669 (m) REVERT: A 331 ASN cc_start: 0.8027 (m-40) cc_final: 0.7664 (m110) REVERT: B 219 ARG cc_start: 0.8784 (mmm-85) cc_final: 0.8520 (mtt-85) REVERT: B 247 ASP cc_start: 0.6956 (t70) cc_final: 0.6610 (t0) REVERT: B 267 ASP cc_start: 0.8345 (m-30) cc_final: 0.8026 (t0) REVERT: B 291 ASP cc_start: 0.7803 (t70) cc_final: 0.7304 (t70) REVERT: B 331 SER cc_start: 0.8806 (OUTLIER) cc_final: 0.8593 (t) REVERT: E 80 PHE cc_start: 0.7928 (m-10) cc_final: 0.7725 (m-80) REVERT: E 140 MET cc_start: 0.8614 (mmm) cc_final: 0.7820 (mmm) REVERT: E 161 SER cc_start: 0.8905 (t) cc_final: 0.8307 (t) REVERT: E 218 ARG cc_start: 0.6710 (mmp-170) cc_final: 0.6393 (mmp-170) REVERT: E 220 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7393 (mp0) outliers start: 43 outliers final: 25 residues processed: 214 average time/residue: 0.2715 time to fit residues: 78.9472 Evaluate side-chains 199 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 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 225 VAL Chi-restraints excluded: chain A residue 263 SER 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 217 MET Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 250 CYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 4 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 63 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 333 GLN B 75 GLN B 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.139748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.102687 restraints weight = 13531.859| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.39 r_work: 0.3141 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 9339 Z= 0.205 Angle : 0.579 8.107 12662 Z= 0.294 Chirality : 0.041 0.150 1450 Planarity : 0.003 0.047 1555 Dihedral : 5.477 57.243 1596 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.89 % Allowed : 15.88 % Favored : 80.23 % 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: 1.22 (0.26), residues: 418 sheet: -0.57 (0.31), residues: 251 loop : -1.25 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 95 HIS 0.004 0.001 HIS R 102 PHE 0.017 0.001 PHE R 163 TYR 0.012 0.001 TYR A 230 ARG 0.004 0.000 ARG C 13 *********************** 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 220 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 1.065 Fit side-chains REVERT: R 161 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.7801 (t80) REVERT: R 191 LEU cc_start: 0.6992 (tp) cc_final: 0.6570 (pp) REVERT: R 300 MET cc_start: 0.8622 (mtt) cc_final: 0.8263 (mtm) REVERT: A 48 THR cc_start: 0.8234 (m) cc_final: 0.7936 (p) REVERT: A 52 GLN cc_start: 0.6840 (OUTLIER) cc_final: 0.6558 (tt0) REVERT: A 306 GLN cc_start: 0.8400 (tp40) cc_final: 0.8109 (tp40) REVERT: A 316 THR cc_start: 0.8041 (p) cc_final: 0.7606 (t) REVERT: A 327 THR cc_start: 0.7910 (p) cc_final: 0.7558 (m) REVERT: A 331 ASN cc_start: 0.8174 (m-40) cc_final: 0.7783 (m110) REVERT: B 172 GLU cc_start: 0.7851 (pm20) cc_final: 0.7062 (pm20) REVERT: B 243 THR cc_start: 0.8993 (m) cc_final: 0.8368 (p) REVERT: B 267 ASP cc_start: 0.8456 (m-30) cc_final: 0.8079 (t0) REVERT: B 291 ASP cc_start: 0.7975 (t70) cc_final: 0.7452 (t70) REVERT: B 297 TRP cc_start: 0.9184 (m100) cc_final: 0.8711 (m100) REVERT: E 80 PHE cc_start: 0.7991 (m-10) cc_final: 0.7783 (m-80) REVERT: E 140 MET cc_start: 0.8737 (mmm) cc_final: 0.7611 (mmm) REVERT: E 161 SER cc_start: 0.9024 (t) cc_final: 0.8581 (p) REVERT: E 218 ARG cc_start: 0.6937 (mmp-170) cc_final: 0.6694 (mmm160) outliers start: 38 outliers final: 26 residues processed: 207 average time/residue: 0.2139 time to fit residues: 61.1583 Evaluate side-chains 199 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 156 LEU Chi-restraints excluded: chain R residue 161 PHE 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 52 GLN Chi-restraints excluded: chain A residue 201 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 263 SER 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 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 250 CYS 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 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: 1.9990 chunk 47 optimal weight: 0.0670 chunk 45 optimal weight: 0.9980 chunk 2 optimal weight: 0.0770 chunk 3 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 7 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.141880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.110811 restraints weight = 13452.098| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.63 r_work: 0.3159 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 9339 Z= 0.168 Angle : 0.571 8.173 12662 Z= 0.289 Chirality : 0.040 0.151 1450 Planarity : 0.003 0.047 1555 Dihedral : 5.122 55.458 1596 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.69 % Allowed : 15.88 % Favored : 80.43 % 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: -0.15 (0.25), residues: 1123 helix: 1.31 (0.26), residues: 421 sheet: -0.52 (0.30), residues: 270 loop : -1.18 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS R 102 PHE 0.010 0.001 PHE E 32 TYR 0.012 0.001 TYR A 230 ARG 0.006 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 223 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 1.052 Fit side-chains REVERT: R 26 ARG cc_start: 0.7392 (ttp-110) cc_final: 0.7160 (ptp-110) REVERT: R 157 THR cc_start: 0.7907 (m) cc_final: 0.7554 (t) REVERT: R 161 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7787 (t80) REVERT: R 179 ASN cc_start: 0.8013 (t0) cc_final: 0.6786 (m110) REVERT: R 191 LEU cc_start: 0.6764 (tp) cc_final: 0.6469 (pp) REVERT: R 300 MET cc_start: 0.8471 (mtt) cc_final: 0.8106 (mtm) REVERT: A 48 THR cc_start: 0.8183 (m) cc_final: 0.7905 (p) REVERT: A 52 GLN cc_start: 0.6864 (OUTLIER) cc_final: 0.6566 (tt0) REVERT: A 242 ARG cc_start: 0.7709 (mtt-85) cc_final: 0.7449 (mtt-85) REVERT: A 306 GLN cc_start: 0.8302 (tp40) cc_final: 0.8067 (tp40) REVERT: A 316 THR cc_start: 0.7768 (p) cc_final: 0.7403 (t) REVERT: A 331 ASN cc_start: 0.7983 (m-40) cc_final: 0.7670 (m110) REVERT: B 207 SER cc_start: 0.8772 (m) cc_final: 0.8445 (p) REVERT: B 219 ARG cc_start: 0.8795 (mmm-85) cc_final: 0.8592 (mmm-85) REVERT: B 234 PHE cc_start: 0.9403 (OUTLIER) cc_final: 0.9051 (m-80) REVERT: B 267 ASP cc_start: 0.8234 (m-30) cc_final: 0.7906 (t0) REVERT: B 291 ASP cc_start: 0.7522 (t70) cc_final: 0.7059 (t70) REVERT: B 297 TRP cc_start: 0.9013 (m100) cc_final: 0.8656 (m100) REVERT: E 140 MET cc_start: 0.8628 (mmm) cc_final: 0.7561 (mmm) REVERT: E 161 SER cc_start: 0.8813 (t) cc_final: 0.8441 (p) REVERT: E 183 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8584 (tt0) outliers start: 36 outliers final: 20 residues processed: 213 average time/residue: 0.2220 time to fit residues: 65.3473 Evaluate side-chains 201 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 THR 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 L residue 8 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 52 GLN 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 79 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU 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 Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 183 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 84 optimal weight: 1.9990 chunk 86 optimal weight: 0.0980 chunk 78 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- 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** 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 = 0.3796 r_free = 0.3796 target = 0.141233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.108478 restraints weight = 13332.910| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.66 r_work: 0.3133 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9339 Z= 0.257 Angle : 0.610 8.837 12662 Z= 0.310 Chirality : 0.041 0.156 1450 Planarity : 0.004 0.048 1555 Dihedral : 5.207 56.308 1596 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.00 % Allowed : 15.78 % Favored : 80.23 % 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: -0.11 (0.25), residues: 1123 helix: 1.32 (0.26), residues: 420 sheet: -0.44 (0.31), residues: 264 loop : -1.17 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 91 HIS 0.006 0.001 HIS R 102 PHE 0.010 0.001 PHE A 189 TYR 0.012 0.001 TYR B 59 ARG 0.007 0.001 ARG E 218 *********************** 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: 39 poor density : 176 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: R 26 ARG cc_start: 0.7444 (ttp-110) cc_final: 0.7242 (ptp-110) REVERT: R 157 THR cc_start: 0.8077 (m) cc_final: 0.7766 (t) REVERT: R 161 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.7900 (t80) REVERT: R 179 ASN cc_start: 0.8080 (t0) cc_final: 0.6826 (m110) REVERT: R 191 LEU cc_start: 0.6795 (tp) cc_final: 0.6515 (pp) REVERT: R 300 MET cc_start: 0.8479 (mtt) cc_final: 0.8127 (mtm) REVERT: A 48 THR cc_start: 0.8290 (m) cc_final: 0.7956 (p) REVERT: A 52 GLN cc_start: 0.6934 (OUTLIER) cc_final: 0.6550 (tt0) REVERT: A 242 ARG cc_start: 0.7849 (mtt-85) cc_final: 0.7626 (mtt-85) REVERT: A 306 GLN cc_start: 0.8322 (tp40) cc_final: 0.8072 (tp40) REVERT: A 316 THR cc_start: 0.7767 (p) cc_final: 0.7361 (t) REVERT: A 327 THR cc_start: 0.7939 (p) cc_final: 0.7526 (m) REVERT: A 331 ASN cc_start: 0.8115 (m-40) cc_final: 0.7731 (m110) REVERT: B 207 SER cc_start: 0.8803 (m) cc_final: 0.8474 (p) REVERT: B 209 LYS cc_start: 0.8989 (mttm) cc_final: 0.8728 (mttp) REVERT: B 234 PHE cc_start: 0.9453 (OUTLIER) cc_final: 0.9031 (m-80) REVERT: B 243 THR cc_start: 0.8884 (m) cc_final: 0.8316 (p) REVERT: B 267 ASP cc_start: 0.8243 (m-30) cc_final: 0.7947 (t0) REVERT: B 291 ASP cc_start: 0.7593 (t70) cc_final: 0.7193 (t70) REVERT: B 297 TRP cc_start: 0.9136 (m100) cc_final: 0.8675 (m100) REVERT: E 89 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7355 (tp30) REVERT: E 140 MET cc_start: 0.8750 (mmm) cc_final: 0.7729 (mmm) REVERT: E 153 GLU cc_start: 0.8100 (pt0) cc_final: 0.7813 (pm20) REVERT: E 161 SER cc_start: 0.8998 (t) cc_final: 0.8630 (p) outliers start: 39 outliers final: 29 residues processed: 204 average time/residue: 0.2211 time to fit residues: 62.1286 Evaluate side-chains 204 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 R residue 234 ILE Chi-restraints excluded: chain L residue 8 VAL 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 263 SER 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 67 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 176 GLN 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 317 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 86 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 3 optimal weight: 0.0170 chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 overall best weight: 0.6218 ------------------------------------------------------------------------------- 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 ** B 340 ASN ** 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 = 0.3798 r_free = 0.3798 target = 0.140950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.108788 restraints weight = 13774.539| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.59 r_work: 0.3137 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 9339 Z= 0.189 Angle : 0.583 7.822 12662 Z= 0.298 Chirality : 0.040 0.150 1450 Planarity : 0.003 0.048 1555 Dihedral : 4.939 55.323 1596 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.38 % Allowed : 16.39 % Favored : 80.23 % 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: 1.31 (0.26), residues: 423 sheet: -0.41 (0.31), residues: 272 loop : -1.08 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 91 HIS 0.004 0.001 HIS R 102 PHE 0.009 0.001 PHE E 32 TYR 0.011 0.001 TYR E 190 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 214 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 157 THR cc_start: 0.8055 (m) cc_final: 0.7758 (t) REVERT: R 161 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7894 (t80) REVERT: R 179 ASN cc_start: 0.8056 (t0) cc_final: 0.6815 (m110) REVERT: R 191 LEU cc_start: 0.6782 (tp) cc_final: 0.6531 (pp) REVERT: R 295 SER cc_start: 0.8707 (OUTLIER) cc_final: 0.8361 (t) REVERT: R 298 ASN cc_start: 0.8431 (m-40) cc_final: 0.8202 (m-40) REVERT: R 300 MET cc_start: 0.8484 (mtt) cc_final: 0.8150 (mtm) REVERT: A 48 THR cc_start: 0.8296 (m) cc_final: 0.7957 (p) REVERT: A 242 ARG cc_start: 0.7897 (mtt-85) cc_final: 0.7649 (mtt-85) REVERT: A 331 ASN cc_start: 0.8108 (m-40) cc_final: 0.7853 (m110) REVERT: B 155 ASN cc_start: 0.7796 (t0) cc_final: 0.7510 (t0) REVERT: B 207 SER cc_start: 0.8741 (m) cc_final: 0.8488 (p) REVERT: B 234 PHE cc_start: 0.9456 (OUTLIER) cc_final: 0.9008 (m-80) REVERT: B 243 THR cc_start: 0.8869 (m) cc_final: 0.8312 (p) REVERT: B 267 ASP cc_start: 0.8210 (m-30) cc_final: 0.7924 (t0) REVERT: B 291 ASP cc_start: 0.7521 (t70) cc_final: 0.7131 (t70) REVERT: B 297 TRP cc_start: 0.9047 (m100) cc_final: 0.8685 (m100) REVERT: E 140 MET cc_start: 0.8678 (mmm) cc_final: 0.7666 (mmm) REVERT: E 161 SER cc_start: 0.8910 (t) cc_final: 0.8587 (p) outliers start: 33 outliers final: 24 residues processed: 207 average time/residue: 0.2197 time to fit residues: 62.4655 Evaluate side-chains 202 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 1.197 ------------------------------------------------------------------------------- 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 R residue 295 SER Chi-restraints excluded: chain L residue 8 VAL 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 176 GLN 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 Chi-restraints excluded: chain E residue 139 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 86 optimal weight: 0.4980 chunk 106 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 44 optimal weight: 0.0370 chunk 103 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 100 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.0062 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.139233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.106893 restraints weight = 13516.098| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.65 r_work: 0.3104 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9339 Z= 0.234 Angle : 0.613 8.281 12662 Z= 0.311 Chirality : 0.041 0.153 1450 Planarity : 0.004 0.049 1555 Dihedral : 4.959 56.526 1596 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.28 % Allowed : 16.91 % Favored : 79.82 % 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: -0.01 (0.25), residues: 1123 helix: 1.31 (0.26), residues: 427 sheet: -0.34 (0.31), residues: 273 loop : -1.08 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP R 91 HIS 0.005 0.001 HIS R 102 PHE 0.009 0.001 PHE A 189 TYR 0.011 0.001 TYR E 190 ARG 0.011 0.001 ARG E 218 *********************** 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 207 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: R 157 THR cc_start: 0.8084 (m) cc_final: 0.7806 (t) REVERT: R 161 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7933 (t80) REVERT: R 179 ASN cc_start: 0.8113 (t0) cc_final: 0.6773 (m110) REVERT: R 191 LEU cc_start: 0.6829 (tp) cc_final: 0.6598 (pp) REVERT: R 295 SER cc_start: 0.8683 (OUTLIER) cc_final: 0.8330 (t) REVERT: R 298 ASN cc_start: 0.8451 (m-40) cc_final: 0.8232 (m-40) REVERT: R 300 MET cc_start: 0.8527 (mtt) cc_final: 0.8190 (mtm) REVERT: A 48 THR cc_start: 0.8249 (m) cc_final: 0.7938 (p) REVERT: A 242 ARG cc_start: 0.7925 (mtt-85) cc_final: 0.7676 (mtt-85) REVERT: A 316 THR cc_start: 0.7852 (p) cc_final: 0.7421 (t) REVERT: B 155 ASN cc_start: 0.7682 (t0) cc_final: 0.7365 (t0) REVERT: B 172 GLU cc_start: 0.7536 (pm20) cc_final: 0.7263 (pm20) REVERT: B 207 SER cc_start: 0.8785 (m) cc_final: 0.8474 (p) REVERT: B 234 PHE cc_start: 0.9465 (OUTLIER) cc_final: 0.8968 (m-80) REVERT: B 243 THR cc_start: 0.8890 (m) cc_final: 0.8327 (p) REVERT: B 267 ASP cc_start: 0.8147 (m-30) cc_final: 0.7848 (t0) REVERT: B 291 ASP cc_start: 0.7573 (t70) cc_final: 0.7192 (t70) REVERT: B 297 TRP cc_start: 0.9096 (m100) cc_final: 0.8693 (m100) REVERT: E 140 MET cc_start: 0.8706 (mmm) cc_final: 0.7725 (mmm) REVERT: E 161 SER cc_start: 0.8938 (t) cc_final: 0.8632 (p) outliers start: 32 outliers final: 27 residues processed: 197 average time/residue: 0.2113 time to fit residues: 57.9408 Evaluate side-chains 200 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 1.099 ------------------------------------------------------------------------------- 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 R residue 234 ILE Chi-restraints excluded: chain R residue 295 SER Chi-restraints excluded: chain L residue 8 VAL 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 263 SER 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 79 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 176 GLN 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 317 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 104 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 35 optimal weight: 0.0170 chunk 25 optimal weight: 3.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- 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 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.140915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.108934 restraints weight = 13771.701| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.70 r_work: 0.3132 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4666 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= 0.197 Angle : 0.604 8.876 12662 Z= 0.306 Chirality : 0.041 0.152 1450 Planarity : 0.003 0.048 1555 Dihedral : 4.824 55.983 1596 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.28 % Allowed : 17.21 % Favored : 79.51 % 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: 1.37 (0.26), residues: 427 sheet: -0.34 (0.30), residues: 285 loop : -0.99 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 91 HIS 0.004 0.001 HIS R 102 PHE 0.009 0.001 PHE E 32 TYR 0.010 0.001 TYR E 190 ARG 0.007 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 206 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 157 THR cc_start: 0.8102 (m) cc_final: 0.7825 (t) REVERT: R 161 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7942 (t80) REVERT: R 179 ASN cc_start: 0.8081 (t0) cc_final: 0.6713 (m110) REVERT: R 191 LEU cc_start: 0.6810 (tp) cc_final: 0.6591 (pp) REVERT: R 295 SER cc_start: 0.8703 (OUTLIER) cc_final: 0.8325 (t) REVERT: R 298 ASN cc_start: 0.8420 (m-40) cc_final: 0.8184 (m-40) REVERT: R 300 MET cc_start: 0.8523 (mtt) cc_final: 0.8193 (mtm) REVERT: A 48 THR cc_start: 0.8243 (m) cc_final: 0.7908 (p) REVERT: A 242 ARG cc_start: 0.7918 (mtt-85) cc_final: 0.7666 (mtt-85) REVERT: B 155 ASN cc_start: 0.7704 (t0) cc_final: 0.7195 (t0) REVERT: B 207 SER cc_start: 0.8748 (m) cc_final: 0.8471 (p) REVERT: B 234 PHE cc_start: 0.9292 (OUTLIER) cc_final: 0.8977 (m-80) REVERT: B 267 ASP cc_start: 0.8112 (m-30) cc_final: 0.7893 (m-30) REVERT: B 291 ASP cc_start: 0.7528 (t70) cc_final: 0.7142 (t70) REVERT: B 297 TRP cc_start: 0.9006 (m100) cc_final: 0.8642 (m100) REVERT: E 140 MET cc_start: 0.8698 (mmm) cc_final: 0.7724 (mmm) REVERT: E 161 SER cc_start: 0.8918 (t) cc_final: 0.8635 (p) outliers start: 32 outliers final: 26 residues processed: 196 average time/residue: 0.2406 time to fit residues: 65.9124 Evaluate side-chains 195 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 R residue 295 SER Chi-restraints excluded: chain L residue 8 VAL 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 263 SER 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 79 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 176 GLN 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 Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 219 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 66 optimal weight: 0.0570 chunk 21 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- 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 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 340 ASN E 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.141153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.104178 restraints weight = 13599.872| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.38 r_work: 0.3156 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 9339 Z= 0.196 Angle : 0.596 7.977 12662 Z= 0.302 Chirality : 0.040 0.153 1450 Planarity : 0.004 0.048 1555 Dihedral : 4.773 56.821 1596 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.87 % Allowed : 17.83 % 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: 0.12 (0.25), residues: 1123 helix: 1.46 (0.26), residues: 423 sheet: -0.33 (0.30), residues: 284 loop : -1.00 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 91 HIS 0.003 0.001 HIS R 102 PHE 0.010 0.001 PHE B 234 TYR 0.010 0.001 TYR E 190 ARG 0.007 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5178.28 seconds wall clock time: 91 minutes 45.42 seconds (5505.42 seconds total)