Starting phenix.real_space_refine on Thu Feb 13 12:56:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t6v_25729/02_2025/7t6v_25729.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t6v_25729/02_2025/7t6v_25729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t6v_25729/02_2025/7t6v_25729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t6v_25729/02_2025/7t6v_25729.map" model { file = "/net/cci-nas-00/data/ceres_data/7t6v_25729/02_2025/7t6v_25729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t6v_25729/02_2025/7t6v_25729.cif" } resolution = 3.1 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= 0.005 sd= 0.048 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 64 5.16 5 C 5734 2.51 5 N 1506 2.21 5 O 1645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8949 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2346 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain: "A" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1753 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: "L" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.20, per 1000 atoms: 0.58 Number of scatterers: 8949 At special positions: 0 Unit cell: (106.029, 106.029, 132.804, 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 64 16.00 O 1645 8.00 N 1506 7.00 C 5734 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 176 " distance=2.08 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 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: 2.26 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... Number of C-beta restraints generated: 2122 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 40.0% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'R' and resid 22 through 53 Proline residue: R 29 - end of helix Processing helix chain 'R' and resid 58 through 77 Processing helix chain 'R' and resid 77 through 87 removed outlier: 4.019A pdb=" N LEU R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 129 removed outlier: 3.584A pdb=" N ASP R 106 " --> pdb=" O HIS R 102 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE R 110 " --> pdb=" O ASP R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 137 Processing helix chain 'R' and resid 138 through 146 Processing helix chain 'R' and resid 146 through 157 removed outlier: 4.079A pdb=" N TRP R 150 " --> pdb=" O ILE R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 157 through 164 removed outlier: 3.590A pdb=" N PHE R 161 " --> pdb=" O THR R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 208 removed outlier: 3.535A pdb=" N THR R 196 " --> pdb=" O LYS R 192 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET R 197 " --> pdb=" O VAL R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 231 Processing helix chain 'R' and resid 237 through 267 removed outlier: 3.855A pdb=" N LEU R 243 " --> pdb=" O PRO R 239 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR R 244 " --> pdb=" O LEU R 240 " (cutoff:3.500A) Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 267 through 275 Processing helix chain 'R' and resid 278 through 303 removed outlier: 3.647A pdb=" N ILE R 282 " --> pdb=" O LYS R 278 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASN R 285 " --> pdb=" O ASP R 281 " (cutoff:3.500A) Proline residue: R 286 - end of helix removed outlier: 3.755A pdb=" N LEU R 290 " --> pdb=" O PRO R 286 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA R 291 " --> pdb=" O THR R 287 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER R 295 " --> pdb=" O ALA R 291 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N CYS R 296 " --> pdb=" O PHE R 292 " (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: 3.898A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 53 removed outlier: 3.551A pdb=" N LYS A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.005A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.001A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.538A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 327 through 351 removed outlier: 3.978A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 24 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.541A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.720A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.561A pdb=" N SER E 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.099A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 208 through 212 removed outlier: 3.546A pdb=" N VAL E 212 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 165 through 168 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.698A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 52 removed outlier: 3.850A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.925A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.748A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.825A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.052A 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: 6.770A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.548A 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: 3.677A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.442A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.319A 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 11 through 12 removed outlier: 5.972A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.345A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.882A pdb=" N GLU E 234 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1296 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: 2.76 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1578 1.32 - 1.45: 2386 1.45 - 1.57: 5081 1.57 - 1.70: 0 1.70 - 1.82: 94 Bond restraints: 9139 Sorted by residual: bond pdb=" CA SER R 84 " pdb=" CB SER R 84 " ideal model delta sigma weight residual 1.528 1.470 0.058 1.56e-02 4.11e+03 1.40e+01 bond pdb=" CA SER R 112 " pdb=" CB SER R 112 " ideal model delta sigma weight residual 1.529 1.473 0.056 1.55e-02 4.16e+03 1.32e+01 bond pdb=" CA SER R 73 " pdb=" CB SER R 73 " ideal model delta sigma weight residual 1.529 1.475 0.054 1.55e-02 4.16e+03 1.21e+01 bond pdb=" N ILE R 195 " pdb=" CA ILE R 195 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.25e-02 6.40e+03 1.20e+01 bond pdb=" CA SER R 211 " pdb=" CB SER R 211 " ideal model delta sigma weight residual 1.530 1.476 0.055 1.58e-02 4.01e+03 1.19e+01 ... (remaining 9134 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 11575 2.39 - 4.77: 738 4.77 - 7.16: 52 7.16 - 9.55: 5 9.55 - 11.94: 3 Bond angle restraints: 12373 Sorted by residual: angle pdb=" C PRO R 92 " pdb=" CA PRO R 92 " pdb=" CB PRO R 92 " ideal model delta sigma weight residual 112.64 100.70 11.94 1.43e+00 4.89e-01 6.97e+01 angle pdb=" CA PHE B 235 " pdb=" CB PHE B 235 " pdb=" CG PHE B 235 " ideal model delta sigma weight residual 113.80 120.19 -6.39 1.00e+00 1.00e+00 4.08e+01 angle pdb=" C PHE R 161 " pdb=" CA PHE R 161 " pdb=" CB PHE R 161 " ideal model delta sigma weight residual 110.88 101.62 9.26 1.57e+00 4.06e-01 3.48e+01 angle pdb=" C LYS R 99 " pdb=" CA LYS R 99 " pdb=" CB LYS R 99 " ideal model delta sigma weight residual 110.85 120.76 -9.91 1.70e+00 3.46e-01 3.40e+01 angle pdb=" C TYR R 302 " pdb=" N VAL R 303 " pdb=" CA VAL R 303 " ideal model delta sigma weight residual 122.77 116.71 6.06 1.05e+00 9.07e-01 3.33e+01 ... (remaining 12368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 4918 16.49 - 32.99: 396 32.99 - 49.48: 67 49.48 - 65.97: 10 65.97 - 82.46: 8 Dihedral angle restraints: 5399 sinusoidal: 2108 harmonic: 3291 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 -163.28 77.28 1 1.00e+01 1.00e-02 7.49e+01 dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 163.97 -70.97 1 1.00e+01 1.00e-02 6.47e+01 dihedral pdb=" C LYS R 99 " pdb=" N LYS R 99 " pdb=" CA LYS R 99 " pdb=" CB LYS R 99 " ideal model delta harmonic sigma weight residual -122.60 -138.12 15.52 0 2.50e+00 1.60e-01 3.86e+01 ... (remaining 5396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1078 0.102 - 0.205: 303 0.205 - 0.307: 26 0.307 - 0.409: 4 0.409 - 0.512: 1 Chirality restraints: 1412 Sorted by residual: chirality pdb=" CA LYS R 99 " pdb=" N LYS R 99 " pdb=" C LYS R 99 " pdb=" CB LYS R 99 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.54e+00 chirality pdb=" CA ASP R 106 " pdb=" N ASP R 106 " pdb=" C ASP R 106 " pdb=" CB ASP R 106 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CA ASN R 135 " pdb=" N ASN R 135 " pdb=" C ASN R 135 " pdb=" CB ASN R 135 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 1409 not shown) Planarity restraints: 1553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG R 205 " -0.020 2.00e-02 2.50e+03 4.19e-02 1.76e+01 pdb=" C ARG R 205 " 0.073 2.00e-02 2.50e+03 pdb=" O ARG R 205 " -0.027 2.00e-02 2.50e+03 pdb=" N PHE R 206 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO R 299 " -0.017 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C PRO R 299 " 0.061 2.00e-02 2.50e+03 pdb=" O PRO R 299 " -0.023 2.00e-02 2.50e+03 pdb=" N MET R 300 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 183 " 0.027 2.00e-02 2.50e+03 1.82e-02 8.28e+00 pdb=" CG TRP R 183 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP R 183 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP R 183 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP R 183 " 0.033 2.00e-02 2.50e+03 pdb=" CE2 TRP R 183 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP R 183 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 183 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 183 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP R 183 " 0.000 2.00e-02 2.50e+03 ... (remaining 1550 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 85 2.62 - 3.19: 7877 3.19 - 3.76: 13170 3.76 - 4.33: 18862 4.33 - 4.90: 31124 Nonbonded interactions: 71118 Sorted by model distance: nonbonded pdb=" O ILE L 4 " pdb=" OXT ILE L 5 " model vdw 2.047 3.040 nonbonded pdb=" O THR A 262 " pdb=" NZ LYS A 317 " model vdw 2.268 3.120 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.319 3.040 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.319 3.120 nonbonded pdb=" OE2 GLU A 308 " pdb=" OG1 THR A 321 " model vdw 2.325 3.040 ... (remaining 71113 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: 0.400 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.470 Find NCS groups from input model: 0.100 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 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 : 0.011 0.058 9139 Z= 0.696 Angle : 1.265 11.936 12373 Z= 0.933 Chirality : 0.089 0.512 1412 Planarity : 0.006 0.054 1553 Dihedral : 12.331 82.461 3271 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.10 % Allowed : 4.00 % Favored : 95.90 % Cbeta Deviations : 0.28 % 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: 1.19 (0.24), residues: 1123 helix: 2.04 (0.24), residues: 402 sheet: 0.60 (0.30), residues: 278 loop : -0.19 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP R 183 HIS 0.012 0.002 HIS R 136 PHE 0.033 0.002 PHE B 235 TYR 0.022 0.002 TYR R 302 ARG 0.008 0.001 ARG R 54 *********************** 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 270 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 269 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: R 77 THR cc_start: 0.8744 (t) cc_final: 0.8414 (p) REVERT: R 103 ILE cc_start: 0.8263 (mm) cc_final: 0.8023 (mt) REVERT: R 161 PHE cc_start: 0.8002 (m-80) cc_final: 0.7785 (m-80) REVERT: R 229 HIS cc_start: 0.7711 (t-90) cc_final: 0.7482 (t-170) REVERT: R 278 LYS cc_start: 0.8922 (mmmt) cc_final: 0.8611 (mmmt) REVERT: R 281 ASP cc_start: 0.7515 (m-30) cc_final: 0.7149 (m-30) REVERT: A 209 LYS cc_start: 0.8085 (mttt) cc_final: 0.7885 (mttt) REVERT: A 271 LYS cc_start: 0.8055 (ttpp) cc_final: 0.7851 (ttpp) REVERT: A 275 GLU cc_start: 0.8400 (tp30) cc_final: 0.8074 (tp30) REVERT: A 309 ASP cc_start: 0.8277 (t70) cc_final: 0.7985 (t70) REVERT: B 45 MET cc_start: 0.8520 (mtt) cc_final: 0.8295 (mtt) REVERT: B 215 GLU cc_start: 0.7986 (mp0) cc_final: 0.7173 (mp0) REVERT: B 233 CYS cc_start: 0.7807 (t) cc_final: 0.7568 (t) REVERT: B 258 ASP cc_start: 0.7777 (t0) cc_final: 0.7333 (t0) REVERT: B 259 GLN cc_start: 0.7507 (tt0) cc_final: 0.7294 (tt0) outliers start: 1 outliers final: 1 residues processed: 270 average time/residue: 0.2776 time to fit residues: 95.6659 Evaluate side-chains 239 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 238 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 119 ASN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.103664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.089331 restraints weight = 14720.058| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.42 r_work: 0.3133 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9139 Z= 0.254 Angle : 0.597 9.520 12373 Z= 0.319 Chirality : 0.044 0.188 1412 Planarity : 0.005 0.047 1553 Dihedral : 4.774 54.325 1245 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.85 % Allowed : 10.15 % Favored : 88.00 % 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: 1.13 (0.24), residues: 1123 helix: 1.98 (0.25), residues: 406 sheet: 0.61 (0.30), residues: 267 loop : -0.25 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 95 HIS 0.005 0.001 HIS B 311 PHE 0.023 0.002 PHE R 161 TYR 0.019 0.001 TYR R 175 ARG 0.005 0.001 ARG R 310 *********************** 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 277 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 259 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 57 ARG cc_start: 0.9138 (tpp80) cc_final: 0.8929 (tpp80) REVERT: R 74 PHE cc_start: 0.8197 (t80) cc_final: 0.7890 (t80) REVERT: R 77 THR cc_start: 0.8846 (t) cc_final: 0.8622 (p) REVERT: R 83 VAL cc_start: 0.8684 (t) cc_final: 0.8468 (m) REVERT: R 91 TRP cc_start: 0.9002 (t-100) cc_final: 0.8575 (t-100) REVERT: R 106 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.8142 (t0) REVERT: R 189 GLU cc_start: 0.8553 (tm-30) cc_final: 0.7997 (tm-30) REVERT: R 235 LYS cc_start: 0.8591 (pttp) cc_final: 0.8219 (pttp) REVERT: R 241 ARG cc_start: 0.7117 (tmt170) cc_final: 0.6858 (ttp-170) REVERT: R 312 ARG cc_start: 0.8339 (tpp80) cc_final: 0.7985 (tpp80) REVERT: A 197 LYS cc_start: 0.8346 (mmmt) cc_final: 0.8062 (mtpp) REVERT: A 209 LYS cc_start: 0.8687 (mttt) cc_final: 0.8483 (mttt) REVERT: A 275 GLU cc_start: 0.8602 (tp30) cc_final: 0.8325 (tp30) REVERT: A 298 GLU cc_start: 0.7259 (tt0) cc_final: 0.7010 (tt0) REVERT: A 309 ASP cc_start: 0.8430 (t70) cc_final: 0.8051 (t70) REVERT: B 10 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8303 (tm-30) REVERT: B 212 ASP cc_start: 0.8482 (t0) cc_final: 0.7667 (t0) REVERT: B 215 GLU cc_start: 0.8648 (mp0) cc_final: 0.8021 (mp0) REVERT: B 233 CYS cc_start: 0.8750 (t) cc_final: 0.8474 (t) REVERT: B 258 ASP cc_start: 0.8252 (t0) cc_final: 0.7866 (t0) REVERT: B 294 CYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7935 (t) outliers start: 18 outliers final: 9 residues processed: 265 average time/residue: 0.2910 time to fit residues: 98.0704 Evaluate side-chains 248 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 237 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 82 ILE Chi-restraints excluded: chain R residue 106 ASP Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 66 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 35 optimal weight: 0.0030 chunk 101 optimal weight: 0.0060 chunk 72 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.7808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.104361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.090042 restraints weight = 14722.745| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.45 r_work: 0.3144 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9139 Z= 0.184 Angle : 0.542 9.718 12373 Z= 0.283 Chirality : 0.042 0.180 1412 Planarity : 0.004 0.042 1553 Dihedral : 4.594 58.547 1243 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.54 % Allowed : 14.05 % Favored : 84.41 % 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: 1.08 (0.25), residues: 1123 helix: 1.97 (0.26), residues: 407 sheet: 0.47 (0.30), residues: 266 loop : -0.23 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 95 HIS 0.004 0.001 HIS A 188 PHE 0.025 0.001 PHE R 180 TYR 0.021 0.001 TYR A 296 ARG 0.008 0.001 ARG B 46 *********************** 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 272 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 257 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 83 VAL cc_start: 0.8672 (t) cc_final: 0.8441 (m) REVERT: R 87 MET cc_start: 0.8718 (mtt) cc_final: 0.8398 (mtm) REVERT: R 189 GLU cc_start: 0.8541 (tm-30) cc_final: 0.7983 (tm-30) REVERT: R 231 LYS cc_start: 0.8866 (mttm) cc_final: 0.8565 (ttmm) REVERT: R 241 ARG cc_start: 0.7045 (tmt170) cc_final: 0.6734 (ttp-170) REVERT: R 310 ARG cc_start: 0.8699 (mtm-85) cc_final: 0.8296 (mtm110) REVERT: R 312 ARG cc_start: 0.8385 (tpp80) cc_final: 0.8178 (tpp80) REVERT: A 197 LYS cc_start: 0.8356 (mmmt) cc_final: 0.8130 (mtpp) REVERT: A 209 LYS cc_start: 0.8553 (mttt) cc_final: 0.8351 (mttt) REVERT: A 275 GLU cc_start: 0.8662 (tp30) cc_final: 0.8321 (tp30) REVERT: A 298 GLU cc_start: 0.7341 (tt0) cc_final: 0.7073 (tt0) REVERT: A 309 ASP cc_start: 0.8380 (t70) cc_final: 0.7972 (t70) REVERT: B 13 GLN cc_start: 0.8614 (tt0) cc_final: 0.8076 (tm-30) REVERT: B 212 ASP cc_start: 0.8473 (t0) cc_final: 0.7543 (t0) REVERT: B 215 GLU cc_start: 0.8641 (mp0) cc_final: 0.7939 (mp0) REVERT: B 233 CYS cc_start: 0.8729 (t) cc_final: 0.8439 (t) REVERT: B 258 ASP cc_start: 0.8260 (t0) cc_final: 0.7833 (t0) REVERT: B 294 CYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7976 (t) REVERT: E 67 ARG cc_start: 0.8018 (ptt90) cc_final: 0.7746 (ptt-90) outliers start: 15 outliers final: 8 residues processed: 265 average time/residue: 0.2966 time to fit residues: 100.1123 Evaluate side-chains 241 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 232 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 294 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 3 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.102758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.088587 restraints weight = 14655.672| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.43 r_work: 0.3118 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9139 Z= 0.238 Angle : 0.551 8.417 12373 Z= 0.288 Chirality : 0.042 0.184 1412 Planarity : 0.004 0.040 1553 Dihedral : 4.540 50.182 1243 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.95 % Allowed : 14.56 % Favored : 83.49 % 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: 1.01 (0.25), residues: 1123 helix: 1.91 (0.26), residues: 408 sheet: 0.35 (0.29), residues: 277 loop : -0.23 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 95 HIS 0.003 0.001 HIS A 213 PHE 0.021 0.002 PHE R 180 TYR 0.020 0.001 TYR A 296 ARG 0.009 0.000 ARG B 46 *********************** 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 278 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 259 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 83 VAL cc_start: 0.8638 (t) cc_final: 0.8389 (m) REVERT: R 87 MET cc_start: 0.8759 (mtt) cc_final: 0.8432 (mtm) REVERT: R 189 GLU cc_start: 0.8569 (tm-30) cc_final: 0.7968 (tm-30) REVERT: R 203 ILE cc_start: 0.8850 (tt) cc_final: 0.8477 (mm) REVERT: R 205 ARG cc_start: 0.8677 (ttp-110) cc_final: 0.8473 (ttp-170) REVERT: R 235 LYS cc_start: 0.8588 (pttp) cc_final: 0.8213 (pttp) REVERT: R 241 ARG cc_start: 0.7151 (tmt170) cc_final: 0.6756 (ttp-170) REVERT: R 310 ARG cc_start: 0.8744 (mtm-85) cc_final: 0.8250 (mtm110) REVERT: A 189 PHE cc_start: 0.8739 (p90) cc_final: 0.8344 (p90) REVERT: A 197 LYS cc_start: 0.8396 (mmmt) cc_final: 0.8143 (mtpp) REVERT: A 275 GLU cc_start: 0.8636 (tp30) cc_final: 0.8337 (tp30) REVERT: A 298 GLU cc_start: 0.7364 (tt0) cc_final: 0.7068 (tt0) REVERT: A 309 ASP cc_start: 0.8389 (t70) cc_final: 0.7982 (t70) REVERT: B 212 ASP cc_start: 0.8514 (t0) cc_final: 0.7585 (t0) REVERT: B 215 GLU cc_start: 0.8659 (mp0) cc_final: 0.7921 (mp0) REVERT: B 233 CYS cc_start: 0.8767 (t) cc_final: 0.8499 (t) REVERT: B 258 ASP cc_start: 0.8280 (t0) cc_final: 0.7901 (t0) REVERT: B 294 CYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7950 (t) REVERT: B 336 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8359 (mp) REVERT: E 234 GLU cc_start: 0.7712 (pm20) cc_final: 0.6879 (pm20) outliers start: 19 outliers final: 13 residues processed: 269 average time/residue: 0.2935 time to fit residues: 100.5349 Evaluate side-chains 257 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 242 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 271 MET Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 142 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 64 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.102433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.088292 restraints weight = 14626.952| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.40 r_work: 0.3115 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9139 Z= 0.247 Angle : 0.561 8.493 12373 Z= 0.290 Chirality : 0.043 0.196 1412 Planarity : 0.004 0.045 1553 Dihedral : 4.508 43.336 1243 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.36 % Allowed : 15.69 % Favored : 81.95 % 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: 0.94 (0.25), residues: 1123 helix: 1.86 (0.26), residues: 408 sheet: 0.27 (0.29), residues: 285 loop : -0.25 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 91 HIS 0.003 0.001 HIS B 311 PHE 0.024 0.002 PHE R 161 TYR 0.022 0.001 TYR A 296 ARG 0.011 0.001 ARG B 46 *********************** 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 273 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 250 time to evaluate : 1.160 Fit side-chains revert: symmetry clash REVERT: R 54 ARG cc_start: 0.8205 (mmm160) cc_final: 0.7908 (mmm-85) REVERT: R 83 VAL cc_start: 0.8665 (t) cc_final: 0.8412 (m) REVERT: R 87 MET cc_start: 0.8754 (mtt) cc_final: 0.8436 (mtm) REVERT: R 91 TRP cc_start: 0.9117 (t-100) cc_final: 0.8905 (t-100) REVERT: R 106 ASP cc_start: 0.8572 (t0) cc_final: 0.8291 (t0) REVERT: R 189 GLU cc_start: 0.8496 (tm-30) cc_final: 0.7899 (tm-30) REVERT: R 203 ILE cc_start: 0.8889 (tt) cc_final: 0.8585 (mm) REVERT: R 231 LYS cc_start: 0.8865 (mttm) cc_final: 0.8602 (ttmm) REVERT: R 235 LYS cc_start: 0.8557 (pttp) cc_final: 0.8182 (pttp) REVERT: R 241 ARG cc_start: 0.7056 (tmt170) cc_final: 0.6710 (ttp-170) REVERT: A 197 LYS cc_start: 0.8412 (mmmt) cc_final: 0.7983 (mttm) REVERT: A 275 GLU cc_start: 0.8640 (tp30) cc_final: 0.8325 (tp30) REVERT: A 298 GLU cc_start: 0.7375 (tt0) cc_final: 0.7076 (tt0) REVERT: B 212 ASP cc_start: 0.8565 (t0) cc_final: 0.7778 (t0) REVERT: B 215 GLU cc_start: 0.8701 (mp0) cc_final: 0.8001 (mp0) REVERT: B 233 CYS cc_start: 0.8710 (t) cc_final: 0.8423 (t) REVERT: B 258 ASP cc_start: 0.8386 (t0) cc_final: 0.8004 (t0) REVERT: B 336 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8396 (mp) REVERT: E 234 GLU cc_start: 0.7751 (pm20) cc_final: 0.6923 (pm20) outliers start: 23 outliers final: 17 residues processed: 261 average time/residue: 0.2974 time to fit residues: 99.8281 Evaluate side-chains 264 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 246 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 271 MET Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 142 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 101 optimal weight: 0.4980 chunk 86 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 28 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.103316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.089200 restraints weight = 14578.798| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.40 r_work: 0.3134 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9139 Z= 0.200 Angle : 0.549 8.665 12373 Z= 0.284 Chirality : 0.042 0.199 1412 Planarity : 0.004 0.046 1553 Dihedral : 4.327 32.918 1243 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.15 % Allowed : 16.21 % Favored : 81.64 % 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: 0.98 (0.25), residues: 1123 helix: 1.90 (0.26), residues: 409 sheet: 0.24 (0.29), residues: 282 loop : -0.19 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 95 HIS 0.004 0.001 HIS A 188 PHE 0.029 0.001 PHE R 161 TYR 0.020 0.001 TYR A 296 ARG 0.010 0.001 ARG B 46 *********************** 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 267 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 246 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 83 VAL cc_start: 0.8667 (t) cc_final: 0.8408 (m) REVERT: R 87 MET cc_start: 0.8742 (mtt) cc_final: 0.8424 (mtm) REVERT: R 189 GLU cc_start: 0.8500 (tm-30) cc_final: 0.7890 (tm-30) REVERT: R 203 ILE cc_start: 0.8874 (tt) cc_final: 0.8595 (mm) REVERT: R 235 LYS cc_start: 0.8539 (pttp) cc_final: 0.8167 (pttp) REVERT: R 241 ARG cc_start: 0.6978 (tmt170) cc_final: 0.6644 (ttp-170) REVERT: R 310 ARG cc_start: 0.8708 (mtm-85) cc_final: 0.8358 (mtm110) REVERT: A 52 GLN cc_start: 0.8468 (mt0) cc_final: 0.8213 (mt0) REVERT: A 197 LYS cc_start: 0.8437 (mmmt) cc_final: 0.8032 (mttm) REVERT: A 232 LEU cc_start: 0.8863 (mt) cc_final: 0.8624 (mp) REVERT: A 275 GLU cc_start: 0.8626 (tp30) cc_final: 0.8309 (tp30) REVERT: A 298 GLU cc_start: 0.7375 (tt0) cc_final: 0.7063 (tt0) REVERT: B 189 SER cc_start: 0.8648 (p) cc_final: 0.8397 (t) REVERT: B 212 ASP cc_start: 0.8502 (t0) cc_final: 0.7737 (t0) REVERT: B 215 GLU cc_start: 0.8728 (mp0) cc_final: 0.8033 (mp0) REVERT: B 233 CYS cc_start: 0.8689 (t) cc_final: 0.8391 (t) REVERT: B 254 ASP cc_start: 0.8224 (t0) cc_final: 0.7660 (t0) REVERT: B 258 ASP cc_start: 0.8332 (t0) cc_final: 0.7913 (t0) REVERT: B 336 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8389 (mp) REVERT: E 234 GLU cc_start: 0.7773 (pm20) cc_final: 0.7044 (pm20) outliers start: 21 outliers final: 15 residues processed: 256 average time/residue: 0.2858 time to fit residues: 94.0066 Evaluate side-chains 256 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 240 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 271 MET Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 142 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 chunk 68 optimal weight: 0.0970 chunk 85 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.104198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.090027 restraints weight = 14788.826| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.44 r_work: 0.3143 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9139 Z= 0.176 Angle : 0.554 9.203 12373 Z= 0.284 Chirality : 0.041 0.197 1412 Planarity : 0.004 0.050 1553 Dihedral : 4.208 33.128 1243 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.05 % Allowed : 17.33 % Favored : 80.62 % 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: 1.04 (0.25), residues: 1123 helix: 1.96 (0.26), residues: 409 sheet: 0.27 (0.29), residues: 287 loop : -0.18 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 254 HIS 0.004 0.001 HIS A 188 PHE 0.034 0.001 PHE R 161 TYR 0.020 0.001 TYR A 296 ARG 0.012 0.001 ARG B 46 *********************** 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 264 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 244 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 83 VAL cc_start: 0.8659 (t) cc_final: 0.8406 (m) REVERT: R 91 TRP cc_start: 0.9077 (t-100) cc_final: 0.8807 (t-100) REVERT: R 189 GLU cc_start: 0.8487 (tm-30) cc_final: 0.7887 (tm-30) REVERT: R 203 ILE cc_start: 0.8853 (tt) cc_final: 0.8581 (mm) REVERT: R 235 LYS cc_start: 0.8552 (pttp) cc_final: 0.8190 (pttp) REVERT: R 241 ARG cc_start: 0.7175 (tmt170) cc_final: 0.6803 (ttp-170) REVERT: R 310 ARG cc_start: 0.8746 (mtm-85) cc_final: 0.8358 (mtm110) REVERT: A 8 GLU cc_start: 0.7355 (tt0) cc_final: 0.7143 (tt0) REVERT: A 52 GLN cc_start: 0.8497 (mt0) cc_final: 0.8233 (mt0) REVERT: A 197 LYS cc_start: 0.8424 (mmmt) cc_final: 0.8004 (tttp) REVERT: A 232 LEU cc_start: 0.8834 (mt) cc_final: 0.8606 (mp) REVERT: A 275 GLU cc_start: 0.8639 (tp30) cc_final: 0.8238 (tp30) REVERT: A 298 GLU cc_start: 0.7367 (tt0) cc_final: 0.7057 (tt0) REVERT: B 189 SER cc_start: 0.8525 (p) cc_final: 0.8266 (t) REVERT: B 212 ASP cc_start: 0.8497 (t0) cc_final: 0.7612 (t0) REVERT: B 215 GLU cc_start: 0.8728 (mp0) cc_final: 0.8026 (mp0) REVERT: B 233 CYS cc_start: 0.8684 (t) cc_final: 0.8386 (t) REVERT: B 254 ASP cc_start: 0.8212 (t0) cc_final: 0.7694 (t0) REVERT: B 258 ASP cc_start: 0.8306 (t0) cc_final: 0.7894 (t0) REVERT: B 336 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8409 (mp) REVERT: E 128 MET cc_start: 0.9189 (mmm) cc_final: 0.8276 (mmm) REVERT: E 234 GLU cc_start: 0.7791 (pm20) cc_final: 0.7049 (pm20) outliers start: 20 outliers final: 15 residues processed: 257 average time/residue: 0.2776 time to fit residues: 91.8590 Evaluate side-chains 250 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 234 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain L residue 4 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 38 optimal weight: 5.9990 chunk 25 optimal weight: 0.0030 chunk 32 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 62 optimal weight: 0.1980 chunk 108 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.104936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.090661 restraints weight = 14837.247| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.43 r_work: 0.3155 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9139 Z= 0.165 Angle : 0.555 9.415 12373 Z= 0.285 Chirality : 0.041 0.202 1412 Planarity : 0.004 0.054 1553 Dihedral : 4.150 33.384 1243 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.64 % Allowed : 18.46 % Favored : 79.90 % 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: 1.13 (0.25), residues: 1123 helix: 2.02 (0.26), residues: 410 sheet: 0.33 (0.30), residues: 280 loop : -0.11 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 254 HIS 0.004 0.001 HIS A 188 PHE 0.033 0.002 PHE R 163 TYR 0.018 0.001 TYR A 296 ARG 0.014 0.001 ARG B 46 *********************** 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 269 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 253 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 83 VAL cc_start: 0.8668 (t) cc_final: 0.8398 (m) REVERT: R 87 MET cc_start: 0.8603 (mtt) cc_final: 0.8329 (mtm) REVERT: R 189 GLU cc_start: 0.8497 (tm-30) cc_final: 0.7894 (tm-30) REVERT: R 203 ILE cc_start: 0.8867 (tt) cc_final: 0.8594 (mm) REVERT: R 229 HIS cc_start: 0.8159 (t70) cc_final: 0.7934 (t70) REVERT: R 241 ARG cc_start: 0.7139 (tmt170) cc_final: 0.6745 (ttp-170) REVERT: R 252 ILE cc_start: 0.8730 (mm) cc_final: 0.8491 (mt) REVERT: R 292 PHE cc_start: 0.8512 (m-10) cc_final: 0.8284 (m-10) REVERT: R 310 ARG cc_start: 0.8773 (mtm-85) cc_final: 0.8359 (mtm110) REVERT: A 52 GLN cc_start: 0.8487 (mt0) cc_final: 0.8209 (mt0) REVERT: A 197 LYS cc_start: 0.8388 (mmmt) cc_final: 0.8016 (tttp) REVERT: A 232 LEU cc_start: 0.8826 (mt) cc_final: 0.8613 (mp) REVERT: A 298 GLU cc_start: 0.7344 (tt0) cc_final: 0.7034 (tt0) REVERT: A 309 ASP cc_start: 0.8400 (t0) cc_final: 0.8072 (t70) REVERT: B 212 ASP cc_start: 0.8489 (t0) cc_final: 0.7604 (t0) REVERT: B 215 GLU cc_start: 0.8702 (mp0) cc_final: 0.7971 (mp0) REVERT: B 233 CYS cc_start: 0.8675 (t) cc_final: 0.8373 (t) REVERT: B 254 ASP cc_start: 0.8222 (t0) cc_final: 0.7717 (t0) REVERT: B 258 ASP cc_start: 0.8277 (t0) cc_final: 0.7862 (t0) REVERT: B 336 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8439 (mp) REVERT: E 128 MET cc_start: 0.9195 (mmm) cc_final: 0.8280 (mmm) REVERT: E 132 THR cc_start: 0.8401 (m) cc_final: 0.8100 (t) REVERT: E 218 MET cc_start: 0.8414 (tpp) cc_final: 0.8003 (tpp) REVERT: E 234 GLU cc_start: 0.7815 (pm20) cc_final: 0.7096 (pm20) outliers start: 16 outliers final: 13 residues processed: 262 average time/residue: 0.2787 time to fit residues: 95.0300 Evaluate side-chains 256 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 242 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 142 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 68 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.103928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.089761 restraints weight = 14818.983| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.43 r_work: 0.3139 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9139 Z= 0.201 Angle : 0.574 9.829 12373 Z= 0.294 Chirality : 0.042 0.193 1412 Planarity : 0.004 0.042 1553 Dihedral : 4.179 33.767 1243 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.54 % Allowed : 19.38 % Favored : 79.08 % 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: 1.05 (0.25), residues: 1123 helix: 2.02 (0.26), residues: 410 sheet: 0.19 (0.29), residues: 292 loop : -0.15 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 254 HIS 0.004 0.001 HIS A 188 PHE 0.035 0.002 PHE R 163 TYR 0.018 0.001 TYR A 296 ARG 0.008 0.001 ARG C 27 *********************** 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 256 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 241 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 26 ARG cc_start: 0.8600 (mmm-85) cc_final: 0.8396 (mmm-85) REVERT: R 83 VAL cc_start: 0.8667 (t) cc_final: 0.8391 (m) REVERT: R 87 MET cc_start: 0.8659 (mtt) cc_final: 0.8399 (mtm) REVERT: R 91 TRP cc_start: 0.9055 (t-100) cc_final: 0.8851 (t-100) REVERT: R 189 GLU cc_start: 0.8500 (tm-30) cc_final: 0.7892 (tm-30) REVERT: R 203 ILE cc_start: 0.8873 (tt) cc_final: 0.8627 (mm) REVERT: R 231 LYS cc_start: 0.8913 (ttmm) cc_final: 0.8667 (ttmm) REVERT: R 241 ARG cc_start: 0.7192 (tmt170) cc_final: 0.6762 (ttp-170) REVERT: R 310 ARG cc_start: 0.8798 (mtm-85) cc_final: 0.8364 (mtm110) REVERT: A 52 GLN cc_start: 0.8435 (mt0) cc_final: 0.8186 (mt0) REVERT: A 197 LYS cc_start: 0.8391 (mmmt) cc_final: 0.8006 (tttp) REVERT: A 232 LEU cc_start: 0.8795 (mt) cc_final: 0.8557 (mp) REVERT: A 298 GLU cc_start: 0.7380 (tt0) cc_final: 0.7058 (tt0) REVERT: B 212 ASP cc_start: 0.8519 (t0) cc_final: 0.7878 (t0) REVERT: B 215 GLU cc_start: 0.8709 (mp0) cc_final: 0.8108 (mp0) REVERT: B 233 CYS cc_start: 0.8700 (t) cc_final: 0.8405 (t) REVERT: B 254 ASP cc_start: 0.8193 (t0) cc_final: 0.7700 (t0) REVERT: B 258 ASP cc_start: 0.8255 (t0) cc_final: 0.7838 (t0) REVERT: B 259 GLN cc_start: 0.8375 (tt0) cc_final: 0.7853 (mt0) REVERT: B 336 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8413 (mp) REVERT: E 128 MET cc_start: 0.9194 (mmm) cc_final: 0.8268 (mmm) REVERT: E 132 THR cc_start: 0.8454 (m) cc_final: 0.8212 (t) REVERT: E 218 MET cc_start: 0.8416 (tpp) cc_final: 0.7985 (tpp) REVERT: E 234 GLU cc_start: 0.7864 (pm20) cc_final: 0.7129 (pm20) outliers start: 15 outliers final: 11 residues processed: 251 average time/residue: 0.2733 time to fit residues: 88.0345 Evaluate side-chains 249 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 237 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain L residue 4 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 37 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.102947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.088826 restraints weight = 14837.607| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.42 r_work: 0.3125 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9139 Z= 0.231 Angle : 0.590 9.889 12373 Z= 0.304 Chirality : 0.043 0.212 1412 Planarity : 0.004 0.060 1553 Dihedral : 4.262 34.017 1243 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.33 % Allowed : 20.00 % Favored : 78.67 % 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: 1.01 (0.25), residues: 1123 helix: 1.99 (0.26), residues: 410 sheet: 0.14 (0.29), residues: 292 loop : -0.16 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 183 HIS 0.004 0.001 HIS A 188 PHE 0.037 0.002 PHE R 163 TYR 0.018 0.001 TYR A 296 ARG 0.015 0.001 ARG B 46 ********************** 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 252 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 239 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 83 VAL cc_start: 0.8689 (t) cc_final: 0.8414 (m) REVERT: R 87 MET cc_start: 0.8784 (mtt) cc_final: 0.8523 (mtm) REVERT: R 91 TRP cc_start: 0.9073 (t-100) cc_final: 0.8593 (t-100) REVERT: R 189 GLU cc_start: 0.8529 (tm-30) cc_final: 0.7899 (tm-30) REVERT: R 203 ILE cc_start: 0.8856 (tt) cc_final: 0.8609 (mm) REVERT: R 231 LYS cc_start: 0.8942 (ttmm) cc_final: 0.8683 (ttmm) REVERT: R 241 ARG cc_start: 0.7155 (tmt170) cc_final: 0.6728 (ttp-170) REVERT: R 310 ARG cc_start: 0.8806 (mtm-85) cc_final: 0.8370 (mtm110) REVERT: A 52 GLN cc_start: 0.8408 (mt0) cc_final: 0.8138 (mt0) REVERT: A 275 GLU cc_start: 0.8593 (tp30) cc_final: 0.8328 (tp30) REVERT: A 298 GLU cc_start: 0.7387 (tt0) cc_final: 0.7074 (tt0) REVERT: B 212 ASP cc_start: 0.8546 (t0) cc_final: 0.7866 (t0) REVERT: B 215 GLU cc_start: 0.8732 (mp0) cc_final: 0.7923 (mp0) REVERT: B 233 CYS cc_start: 0.8724 (t) cc_final: 0.8433 (t) REVERT: B 254 ASP cc_start: 0.8229 (t0) cc_final: 0.7741 (t0) REVERT: B 258 ASP cc_start: 0.8245 (t0) cc_final: 0.7801 (t0) REVERT: B 259 GLN cc_start: 0.8380 (tt0) cc_final: 0.7861 (mt0) REVERT: B 336 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8388 (mp) REVERT: E 128 MET cc_start: 0.9184 (mmm) cc_final: 0.8302 (mmm) REVERT: E 132 THR cc_start: 0.8438 (m) cc_final: 0.8198 (t) REVERT: E 218 MET cc_start: 0.8407 (tpp) cc_final: 0.7956 (tpp) REVERT: E 234 GLU cc_start: 0.7856 (pm20) cc_final: 0.7123 (pm20) outliers start: 13 outliers final: 12 residues processed: 247 average time/residue: 0.2727 time to fit residues: 86.7879 Evaluate side-chains 251 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 238 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain L residue 4 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 101 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 64 optimal weight: 0.4980 chunk 110 optimal weight: 0.6980 chunk 92 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.104344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.090169 restraints weight = 14762.394| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.42 r_work: 0.3146 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9139 Z= 0.185 Angle : 0.577 9.792 12373 Z= 0.294 Chirality : 0.042 0.204 1412 Planarity : 0.004 0.058 1553 Dihedral : 4.157 33.959 1243 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.33 % Allowed : 20.51 % Favored : 78.15 % 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: 1.08 (0.25), residues: 1123 helix: 2.05 (0.26), residues: 410 sheet: 0.15 (0.29), residues: 297 loop : -0.10 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 254 HIS 0.004 0.001 HIS A 188 PHE 0.039 0.001 PHE R 163 TYR 0.017 0.001 TYR A 296 ARG 0.014 0.001 ARG B 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5044.70 seconds wall clock time: 90 minutes 16.61 seconds (5416.61 seconds total)