Starting phenix.real_space_refine on Fri Feb 14 12:14:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f9y_31500/02_2025/7f9y_31500_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f9y_31500/02_2025/7f9y_31500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f9y_31500/02_2025/7f9y_31500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f9y_31500/02_2025/7f9y_31500.map" model { file = "/net/cci-nas-00/data/ceres_data/7f9y_31500/02_2025/7f9y_31500_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f9y_31500/02_2025/7f9y_31500_neut.cif" } resolution = 2.9 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= 0.002 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2178 atoms to isotropic. 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 54 5.16 5 C 5329 2.51 5 N 1439 2.21 5 O 1532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 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: 8354 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1877 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2280 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 12, 'TRANS': 272} Chain breaks: 1 Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.05, per 1000 atoms: 0.60 Number of scatterers: 8354 At special positions: 0 Unit cell: (88.893, 111.384, 127.449, 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 54 16.00 O 1532 8.00 N 1439 7.00 C 5329 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 116 " - pdb=" SG CYS R 198 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 948.3 milliseconds 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1980 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 11 sheets defined 44.1% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 16 through 40 removed outlier: 3.744A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP A 33 " --> pdb=" O GLN A 29 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 230 through 235 removed outlier: 4.323A pdb=" N TRP A 234 " --> pdb=" O GLU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.501A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.903A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 3.539A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.538A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.514A pdb=" N ARG A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'C' and resid 7 through 12 removed outlier: 4.092A pdb=" N GLN C 12 " --> pdb=" O HIS C 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.585A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.591A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 39 through 70 removed outlier: 3.686A pdb=" N ARG R 70 " --> pdb=" O LEU R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 95 removed outlier: 3.644A pdb=" N CYS R 95 " --> pdb=" O LEU R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 105 removed outlier: 3.807A pdb=" N ASP R 99 " --> pdb=" O CYS R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 147 Processing helix chain 'R' and resid 147 through 152 removed outlier: 4.403A pdb=" N LYS R 152 " --> pdb=" O PRO R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 156 through 176 Processing helix chain 'R' and resid 177 through 181 Processing helix chain 'R' and resid 191 through 195 Processing helix chain 'R' and resid 201 through 207 Processing helix chain 'R' and resid 209 through 214 Processing helix chain 'R' and resid 214 through 219 removed outlier: 3.658A pdb=" N ILE R 219 " --> pdb=" O TRP R 215 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 241 removed outlier: 3.606A pdb=" N TYR R 232 " --> pdb=" O LEU R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 289 Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 296 through 323 removed outlier: 4.384A pdb=" N ILE R 300 " --> pdb=" O GLU R 296 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR R 313 " --> pdb=" O PHE R 309 " (cutoff:3.500A) Proline residue: R 320 - end of helix removed outlier: 3.710A pdb=" N TYR R 323 " --> pdb=" O ASN R 319 " (cutoff:3.500A) Processing helix chain 'R' and resid 327 through 334 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.522A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.546A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.904A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.243A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.741A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 4.159A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.523A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.329A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.516A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.160A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 182 through 185 412 hydrogen bonds defined for protein. 1179 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: 2.54 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1347 1.31 - 1.44: 2332 1.44 - 1.57: 4774 1.57 - 1.70: 0 1.70 - 1.83: 75 Bond restraints: 8528 Sorted by residual: bond pdb=" C1 OCA C 101 " pdb=" O1 OCA C 101 " ideal model delta sigma weight residual 1.247 1.185 0.062 2.00e-02 2.50e+03 9.70e+00 bond pdb=" N GLY C 0 " pdb=" CA GLY C 0 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.25e+00 bond pdb=" C13 CLR R 602 " pdb=" C17 CLR R 602 " ideal model delta sigma weight residual 1.550 1.513 0.037 2.00e-02 2.50e+03 3.46e+00 bond pdb=" C13 CLR R 601 " pdb=" C17 CLR R 601 " ideal model delta sigma weight residual 1.550 1.515 0.035 2.00e-02 2.50e+03 3.11e+00 bond pdb=" N GLU A 15 " pdb=" CA GLU A 15 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 ... (remaining 8523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 11377 1.71 - 3.43: 138 3.43 - 5.14: 32 5.14 - 6.86: 10 6.86 - 8.57: 2 Bond angle restraints: 11559 Sorted by residual: angle pdb=" C13 CLR R 601 " pdb=" C17 CLR R 601 " pdb=" C20 CLR R 601 " ideal model delta sigma weight residual 119.60 111.03 8.57 3.00e+00 1.11e-01 8.17e+00 angle pdb=" N LEU R 295 " pdb=" CA LEU R 295 " pdb=" C LEU R 295 " ideal model delta sigma weight residual 114.56 111.04 3.52 1.27e+00 6.20e-01 7.67e+00 angle pdb=" C LEU R 118 " pdb=" N PHE R 119 " pdb=" CA PHE R 119 " ideal model delta sigma weight residual 120.68 116.14 4.54 1.70e+00 3.46e-01 7.14e+00 angle pdb=" N PHE R 119 " pdb=" CA PHE R 119 " pdb=" CB PHE R 119 " ideal model delta sigma weight residual 110.30 114.28 -3.98 1.54e+00 4.22e-01 6.68e+00 angle pdb=" C13 CLR R 602 " pdb=" C17 CLR R 602 " pdb=" C20 CLR R 602 " ideal model delta sigma weight residual 119.60 111.85 7.75 3.00e+00 1.11e-01 6.68e+00 ... (remaining 11554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 4747 17.34 - 34.68: 361 34.68 - 52.02: 51 52.02 - 69.36: 14 69.36 - 86.70: 5 Dihedral angle restraints: 5178 sinusoidal: 2124 harmonic: 3054 Sorted by residual: dihedral pdb=" CA PRO R 39 " pdb=" C PRO R 39 " pdb=" N ALA R 40 " pdb=" CA ALA R 40 " ideal model delta harmonic sigma weight residual -180.00 -161.52 -18.48 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA SER R 218 " pdb=" C SER R 218 " pdb=" N ILE R 219 " pdb=" CA ILE R 219 " ideal model delta harmonic sigma weight residual 180.00 162.67 17.33 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ASP A 252 " pdb=" CB ASP A 252 " pdb=" CG ASP A 252 " pdb=" OD1 ASP A 252 " ideal model delta sinusoidal sigma weight residual -30.00 -85.93 55.93 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 5175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1184 0.067 - 0.134: 124 0.134 - 0.201: 3 0.201 - 0.268: 2 0.268 - 0.335: 2 Chirality restraints: 1315 Sorted by residual: chirality pdb=" C13 CLR R 601 " pdb=" C12 CLR R 601 " pdb=" C14 CLR R 601 " pdb=" C17 CLR R 601 " both_signs ideal model delta sigma weight residual False -2.93 -2.60 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" C13 CLR R 602 " pdb=" C12 CLR R 602 " pdb=" C14 CLR R 602 " pdb=" C17 CLR R 602 " both_signs ideal model delta sigma weight residual False -2.93 -2.61 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" C14 CLR R 601 " pdb=" C13 CLR R 601 " pdb=" C15 CLR R 601 " pdb=" C8 CLR R 601 " both_signs ideal model delta sigma weight residual False -2.32 -2.56 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 1312 not shown) Planarity restraints: 1458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS N 87 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO N 88 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO N 88 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO N 88 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.021 5.00e-02 4.00e+02 3.19e-02 1.62e+00 pdb=" N PRO B 236 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE R 38 " -0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO R 39 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO R 39 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 39 " -0.018 5.00e-02 4.00e+02 ... (remaining 1455 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 56 2.54 - 3.13: 6597 3.13 - 3.72: 12815 3.72 - 4.31: 17693 4.31 - 4.90: 30728 Nonbonded interactions: 67889 Sorted by model distance: nonbonded pdb=" OD1 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 1.951 3.040 nonbonded pdb=" O HIS B 54 " pdb=" OG SER B 334 " model vdw 2.148 3.040 nonbonded pdb=" OG1 THR R 77 " pdb=" OE2 GLU R 140 " model vdw 2.156 3.040 nonbonded pdb=" O PHE G 61 " pdb=" NE ARG G 62 " model vdw 2.158 3.120 nonbonded pdb=" OH TYR R 106 " pdb=" OE1 GLU R 197 " model vdw 2.233 3.040 ... (remaining 67884 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.900 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 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 : 0.003 0.062 8528 Z= 0.169 Angle : 0.551 8.573 11559 Z= 0.306 Chirality : 0.042 0.335 1315 Planarity : 0.003 0.041 1458 Dihedral : 12.549 86.698 3195 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.27), residues: 1033 helix: 1.99 (0.27), residues: 410 sheet: 1.12 (0.35), residues: 214 loop : 0.51 (0.33), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 281 HIS 0.003 0.001 HIS A 357 PHE 0.010 0.001 PHE A 363 TYR 0.007 0.001 TYR R 330 ARG 0.013 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.894 Fit side-chains REVERT: A 29 GLN cc_start: 0.7971 (tp40) cc_final: 0.7717 (mm-40) REVERT: A 221 MET cc_start: 0.8257 (ttp) cc_final: 0.8023 (ttm) REVERT: A 272 ASP cc_start: 0.7143 (m-30) cc_final: 0.6729 (m-30) REVERT: A 284 THR cc_start: 0.8369 (p) cc_final: 0.7905 (t) REVERT: A 336 ARG cc_start: 0.7692 (ttp80) cc_final: 0.7419 (ttt-90) REVERT: A 390 GLU cc_start: 0.6389 (mm-30) cc_final: 0.6152 (mm-30) REVERT: B 214 ARG cc_start: 0.6944 (mpt-90) cc_final: 0.6736 (mmm-85) REVERT: N 29 PHE cc_start: 0.8446 (t80) cc_final: 0.8118 (t80) REVERT: R 85 MET cc_start: 0.7284 (ttm) cc_final: 0.7073 (mtp) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 1.2947 time to fit residues: 279.2797 Evaluate side-chains 175 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 42 optimal weight: 0.0770 chunk 26 optimal weight: 0.3980 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 0.0270 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 292 ASN B 220 GLN B 268 ASN N 31 ASN N 35 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.140853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.123931 restraints weight = 11513.025| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.07 r_work: 0.3509 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8528 Z= 0.174 Angle : 0.547 7.676 11559 Z= 0.287 Chirality : 0.042 0.145 1315 Planarity : 0.004 0.051 1458 Dihedral : 5.756 59.012 1277 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.98 % Allowed : 9.92 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.27), residues: 1033 helix: 2.01 (0.26), residues: 401 sheet: 1.21 (0.34), residues: 221 loop : 0.28 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 47 HIS 0.006 0.001 HIS A 357 PHE 0.018 0.001 PHE R 279 TYR 0.011 0.001 TYR B 59 ARG 0.009 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.897 Fit side-chains REVERT: A 29 GLN cc_start: 0.8156 (tp40) cc_final: 0.7935 (mm-40) REVERT: A 218 ASN cc_start: 0.8450 (m-40) cc_final: 0.8041 (m110) REVERT: A 221 MET cc_start: 0.8557 (ttp) cc_final: 0.8347 (ttm) REVERT: A 272 ASP cc_start: 0.7872 (m-30) cc_final: 0.7530 (m-30) REVERT: A 284 THR cc_start: 0.8598 (p) cc_final: 0.8155 (t) REVERT: A 381 ASP cc_start: 0.8207 (t0) cc_final: 0.7928 (t0) REVERT: A 390 GLU cc_start: 0.7234 (mm-30) cc_final: 0.7000 (mm-30) REVERT: A 391 TYR cc_start: 0.7297 (m-10) cc_final: 0.6818 (m-10) REVERT: B 29 THR cc_start: 0.8340 (OUTLIER) cc_final: 0.7939 (p) REVERT: B 197 ARG cc_start: 0.7594 (mmm-85) cc_final: 0.7278 (mmm-85) REVERT: B 214 ARG cc_start: 0.7593 (mpt-90) cc_final: 0.7160 (mpp80) REVERT: B 219 ARG cc_start: 0.8323 (mtt-85) cc_final: 0.8094 (mmm-85) REVERT: B 262 MET cc_start: 0.8187 (tpp) cc_final: 0.7741 (tpp) REVERT: G 47 GLU cc_start: 0.8133 (tt0) cc_final: 0.7857 (tt0) REVERT: N 29 PHE cc_start: 0.8424 (t80) cc_final: 0.8105 (t80) REVERT: R 65 MET cc_start: 0.7041 (tmm) cc_final: 0.6044 (tmm) REVERT: R 201 THR cc_start: 0.7941 (t) cc_final: 0.7619 (p) REVERT: R 213 MET cc_start: 0.7063 (mtp) cc_final: 0.6562 (mtm) REVERT: R 326 MET cc_start: 0.7729 (mmm) cc_final: 0.7466 (mmm) outliers start: 18 outliers final: 10 residues processed: 192 average time/residue: 1.2311 time to fit residues: 251.2523 Evaluate side-chains 195 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 184 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 119 PHE Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain R residue 308 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 96 optimal weight: 0.1980 chunk 77 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.136272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.118838 restraints weight = 11661.166| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.06 r_work: 0.3423 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8528 Z= 0.252 Angle : 0.555 8.323 11559 Z= 0.291 Chirality : 0.043 0.143 1315 Planarity : 0.004 0.046 1458 Dihedral : 5.653 48.750 1277 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.20 % Allowed : 11.80 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.26), residues: 1033 helix: 1.87 (0.26), residues: 396 sheet: 1.18 (0.35), residues: 211 loop : 0.08 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 47 HIS 0.008 0.001 HIS A 357 PHE 0.024 0.002 PHE R 312 TYR 0.014 0.001 TYR B 59 ARG 0.011 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.975 Fit side-chains REVERT: A 29 GLN cc_start: 0.8274 (tp40) cc_final: 0.8016 (mm-40) REVERT: A 272 ASP cc_start: 0.7897 (m-30) cc_final: 0.7587 (m-30) REVERT: A 283 ARG cc_start: 0.8029 (mtm110) cc_final: 0.7747 (mtm-85) REVERT: A 284 THR cc_start: 0.8580 (p) cc_final: 0.8142 (t) REVERT: A 381 ASP cc_start: 0.8341 (t0) cc_final: 0.7952 (t0) REVERT: B 29 THR cc_start: 0.8312 (p) cc_final: 0.7967 (p) REVERT: B 197 ARG cc_start: 0.7870 (mmm-85) cc_final: 0.7589 (mmm-85) REVERT: B 214 ARG cc_start: 0.7834 (mpt-90) cc_final: 0.7507 (mmm-85) REVERT: B 217 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8269 (ptm) REVERT: B 219 ARG cc_start: 0.8438 (mtt-85) cc_final: 0.8181 (mmm-85) REVERT: B 262 MET cc_start: 0.8110 (tpp) cc_final: 0.7677 (tpp) REVERT: B 335 PHE cc_start: 0.8861 (m-10) cc_final: 0.8449 (m-80) REVERT: G 46 LYS cc_start: 0.8407 (mtpt) cc_final: 0.8203 (mtpt) REVERT: G 47 GLU cc_start: 0.8296 (tt0) cc_final: 0.8053 (tt0) REVERT: N 29 PHE cc_start: 0.8596 (t80) cc_final: 0.8219 (t80) REVERT: R 65 MET cc_start: 0.7170 (tmm) cc_final: 0.6192 (tmm) REVERT: R 199 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7828 (ptt90) REVERT: R 201 THR cc_start: 0.8098 (t) cc_final: 0.7727 (p) REVERT: R 213 MET cc_start: 0.7172 (mtp) cc_final: 0.6732 (mtm) REVERT: R 216 VAL cc_start: 0.8300 (t) cc_final: 0.8047 (p) REVERT: R 270 PHE cc_start: 0.7486 (t80) cc_final: 0.7272 (t80) REVERT: R 326 MET cc_start: 0.7721 (mmm) cc_final: 0.7419 (mmm) outliers start: 29 outliers final: 13 residues processed: 202 average time/residue: 1.2848 time to fit residues: 275.2285 Evaluate side-chains 205 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 190 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 119 PHE Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 199 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 78 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.136160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.119317 restraints weight = 11563.825| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.07 r_work: 0.3439 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8528 Z= 0.206 Angle : 0.517 7.325 11559 Z= 0.273 Chirality : 0.042 0.141 1315 Planarity : 0.004 0.044 1458 Dihedral : 5.454 47.549 1277 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.76 % Allowed : 14.33 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.26), residues: 1033 helix: 1.94 (0.26), residues: 399 sheet: 1.08 (0.35), residues: 213 loop : -0.09 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.017 0.001 PHE R 119 TYR 0.012 0.001 TYR R 330 ARG 0.011 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 0.890 Fit side-chains REVERT: A 29 GLN cc_start: 0.8175 (tp40) cc_final: 0.7862 (mm-40) REVERT: A 33 ASP cc_start: 0.7641 (p0) cc_final: 0.7394 (p0) REVERT: A 272 ASP cc_start: 0.7829 (m-30) cc_final: 0.7508 (m-30) REVERT: A 284 THR cc_start: 0.8680 (p) cc_final: 0.8227 (t) REVERT: A 381 ASP cc_start: 0.8287 (t0) cc_final: 0.7845 (t0) REVERT: B 197 ARG cc_start: 0.7879 (mmm-85) cc_final: 0.7106 (mmm-85) REVERT: B 214 ARG cc_start: 0.7968 (mpt-90) cc_final: 0.7428 (mpp80) REVERT: B 219 ARG cc_start: 0.8408 (mtt-85) cc_final: 0.8162 (mmm-85) REVERT: B 262 MET cc_start: 0.8061 (tpp) cc_final: 0.7621 (tpp) REVERT: B 335 PHE cc_start: 0.8834 (m-10) cc_final: 0.8497 (m-80) REVERT: G 46 LYS cc_start: 0.8376 (mtpt) cc_final: 0.8165 (mtpt) REVERT: G 47 GLU cc_start: 0.8214 (tt0) cc_final: 0.7937 (tt0) REVERT: N 28 THR cc_start: 0.8424 (t) cc_final: 0.8181 (p) REVERT: N 29 PHE cc_start: 0.8580 (t80) cc_final: 0.8149 (t80) REVERT: R 65 MET cc_start: 0.7117 (tmm) cc_final: 0.6162 (tmm) REVERT: R 91 LEU cc_start: 0.7774 (tt) cc_final: 0.7557 (tp) REVERT: R 201 THR cc_start: 0.8050 (t) cc_final: 0.7697 (p) REVERT: R 213 MET cc_start: 0.7138 (mtp) cc_final: 0.6787 (mtm) REVERT: R 216 VAL cc_start: 0.8339 (t) cc_final: 0.8088 (p) REVERT: R 326 MET cc_start: 0.7754 (mmm) cc_final: 0.7422 (mmm) outliers start: 25 outliers final: 13 residues processed: 197 average time/residue: 1.1999 time to fit residues: 251.4329 Evaluate side-chains 194 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 119 PHE Chi-restraints excluded: chain R residue 122 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 86 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 268 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.135562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.118787 restraints weight = 11441.209| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.04 r_work: 0.3436 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8528 Z= 0.224 Angle : 0.523 7.250 11559 Z= 0.275 Chirality : 0.042 0.140 1315 Planarity : 0.004 0.045 1458 Dihedral : 5.475 51.613 1277 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.20 % Allowed : 14.77 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.26), residues: 1033 helix: 1.97 (0.26), residues: 397 sheet: 1.05 (0.35), residues: 213 loop : -0.15 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.002 PHE R 119 TYR 0.012 0.001 TYR R 330 ARG 0.005 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 0.911 Fit side-chains REVERT: A 29 GLN cc_start: 0.8188 (tp40) cc_final: 0.7891 (mm-40) REVERT: A 33 ASP cc_start: 0.7613 (p0) cc_final: 0.7383 (p0) REVERT: A 218 ASN cc_start: 0.8433 (m-40) cc_final: 0.7960 (m110) REVERT: A 272 ASP cc_start: 0.7830 (m-30) cc_final: 0.7526 (m-30) REVERT: A 283 ARG cc_start: 0.7958 (mtp-110) cc_final: 0.7709 (mtm-85) REVERT: A 284 THR cc_start: 0.8664 (p) cc_final: 0.8210 (t) REVERT: A 342 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7290 (ttm110) REVERT: A 381 ASP cc_start: 0.8246 (t0) cc_final: 0.7802 (t0) REVERT: B 197 ARG cc_start: 0.7911 (mmm-85) cc_final: 0.7010 (mmm-85) REVERT: B 214 ARG cc_start: 0.7962 (mpt-90) cc_final: 0.7346 (mpp80) REVERT: B 262 MET cc_start: 0.8071 (tpp) cc_final: 0.7635 (tpp) REVERT: B 335 PHE cc_start: 0.8839 (m-10) cc_final: 0.8449 (m-80) REVERT: G 46 LYS cc_start: 0.8353 (mtpt) cc_final: 0.8145 (mtpt) REVERT: G 47 GLU cc_start: 0.8220 (tt0) cc_final: 0.7992 (tt0) REVERT: N 29 PHE cc_start: 0.8604 (t80) cc_final: 0.8163 (t80) REVERT: R 65 MET cc_start: 0.7149 (tmm) cc_final: 0.6184 (tmm) REVERT: R 199 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7776 (ptt90) REVERT: R 201 THR cc_start: 0.8066 (t) cc_final: 0.7691 (p) REVERT: R 213 MET cc_start: 0.7169 (mtp) cc_final: 0.6834 (mtm) REVERT: R 216 VAL cc_start: 0.8354 (t) cc_final: 0.8106 (p) REVERT: R 326 MET cc_start: 0.7733 (mmm) cc_final: 0.7387 (mmm) outliers start: 29 outliers final: 18 residues processed: 197 average time/residue: 1.1662 time to fit residues: 244.6491 Evaluate side-chains 203 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 119 PHE Chi-restraints excluded: chain R residue 199 ARG Chi-restraints excluded: chain R residue 308 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 26 optimal weight: 0.0070 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 52 optimal weight: 7.9990 overall best weight: 1.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN B 220 GLN B 268 ASN B 340 ASN C 12 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.134304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.117534 restraints weight = 11435.305| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.05 r_work: 0.3388 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8528 Z= 0.266 Angle : 0.544 7.609 11559 Z= 0.286 Chirality : 0.043 0.140 1315 Planarity : 0.004 0.046 1458 Dihedral : 5.591 53.873 1277 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.64 % Allowed : 15.88 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.26), residues: 1033 helix: 1.72 (0.26), residues: 409 sheet: 0.86 (0.35), residues: 219 loop : -0.39 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.020 0.002 PHE R 312 TYR 0.014 0.002 TYR R 303 ARG 0.007 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 0.968 Fit side-chains REVERT: A 29 GLN cc_start: 0.8230 (tp40) cc_final: 0.7944 (mm-40) REVERT: A 33 ASP cc_start: 0.7642 (p0) cc_final: 0.7423 (p0) REVERT: A 272 ASP cc_start: 0.7807 (m-30) cc_final: 0.7505 (m-30) REVERT: A 284 THR cc_start: 0.8688 (p) cc_final: 0.8238 (t) REVERT: A 342 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7331 (ttm110) REVERT: A 381 ASP cc_start: 0.8242 (t0) cc_final: 0.7905 (t0) REVERT: B 197 ARG cc_start: 0.7927 (mmm-85) cc_final: 0.7380 (mtp180) REVERT: B 214 ARG cc_start: 0.7887 (mpt-90) cc_final: 0.7273 (mmm-85) REVERT: B 217 MET cc_start: 0.8577 (ptm) cc_final: 0.8321 (ptm) REVERT: B 262 MET cc_start: 0.8078 (tpp) cc_final: 0.7668 (tpp) REVERT: B 335 PHE cc_start: 0.8860 (m-10) cc_final: 0.8513 (m-80) REVERT: N 29 PHE cc_start: 0.8611 (t80) cc_final: 0.8156 (t80) REVERT: N 38 ARG cc_start: 0.8817 (ptt180) cc_final: 0.8573 (ptt180) REVERT: R 65 MET cc_start: 0.7162 (tmm) cc_final: 0.6208 (tmm) REVERT: R 199 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7788 (ptt90) REVERT: R 216 VAL cc_start: 0.8362 (t) cc_final: 0.8103 (p) REVERT: R 318 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7411 (tt) REVERT: R 326 MET cc_start: 0.7756 (mmm) cc_final: 0.7412 (mmm) outliers start: 33 outliers final: 22 residues processed: 195 average time/residue: 1.3043 time to fit residues: 269.3888 Evaluate side-chains 202 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 119 PHE Chi-restraints excluded: chain R residue 199 ARG Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 318 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 58 optimal weight: 0.4980 chunk 22 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN B 220 GLN B 268 ASN B 340 ASN R 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.135282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.118569 restraints weight = 11502.208| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.06 r_work: 0.3426 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8528 Z= 0.188 Angle : 0.511 7.685 11559 Z= 0.270 Chirality : 0.041 0.139 1315 Planarity : 0.004 0.046 1458 Dihedral : 5.431 55.048 1277 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.86 % Allowed : 16.54 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.26), residues: 1033 helix: 2.03 (0.26), residues: 397 sheet: 0.86 (0.35), residues: 221 loop : -0.26 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.001 PHE R 119 TYR 0.010 0.001 TYR R 303 ARG 0.006 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 176 time to evaluate : 0.947 Fit side-chains REVERT: A 29 GLN cc_start: 0.8234 (tp40) cc_final: 0.7940 (mm-40) REVERT: A 33 ASP cc_start: 0.7681 (p0) cc_final: 0.7444 (p0) REVERT: A 272 ASP cc_start: 0.7823 (m-30) cc_final: 0.7508 (m-30) REVERT: A 284 THR cc_start: 0.8711 (p) cc_final: 0.8274 (t) REVERT: A 381 ASP cc_start: 0.8250 (t0) cc_final: 0.7829 (t0) REVERT: B 197 ARG cc_start: 0.7919 (mmm-85) cc_final: 0.7403 (mtp180) REVERT: B 214 ARG cc_start: 0.7911 (mpt-90) cc_final: 0.7293 (mmm-85) REVERT: B 217 MET cc_start: 0.8610 (ptm) cc_final: 0.8335 (ptm) REVERT: B 262 MET cc_start: 0.8023 (tpp) cc_final: 0.7612 (tpp) REVERT: B 335 PHE cc_start: 0.8829 (m-10) cc_final: 0.8513 (m-80) REVERT: G 46 LYS cc_start: 0.8437 (mtpt) cc_final: 0.8233 (mtpt) REVERT: N 28 THR cc_start: 0.8425 (OUTLIER) cc_final: 0.8204 (p) REVERT: N 29 PHE cc_start: 0.8599 (t80) cc_final: 0.8148 (t80) REVERT: R 65 MET cc_start: 0.7134 (tmm) cc_final: 0.6191 (tmm) REVERT: R 102 ARG cc_start: 0.8466 (ttp-170) cc_final: 0.8256 (ttp-170) REVERT: R 199 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7717 (ptt90) REVERT: R 216 VAL cc_start: 0.8354 (t) cc_final: 0.8101 (p) REVERT: R 326 MET cc_start: 0.7740 (mmm) cc_final: 0.7404 (mmm) outliers start: 35 outliers final: 22 residues processed: 195 average time/residue: 1.3141 time to fit residues: 271.6024 Evaluate side-chains 196 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 119 PHE Chi-restraints excluded: chain R residue 122 VAL Chi-restraints excluded: chain R residue 199 ARG Chi-restraints excluded: chain R residue 308 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 21 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 15 optimal weight: 0.3980 chunk 43 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.134808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.118007 restraints weight = 11580.071| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.07 r_work: 0.3422 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8528 Z= 0.206 Angle : 0.510 8.264 11559 Z= 0.270 Chirality : 0.042 0.140 1315 Planarity : 0.004 0.046 1458 Dihedral : 5.399 56.563 1277 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.42 % Allowed : 17.09 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.26), residues: 1033 helix: 1.86 (0.26), residues: 409 sheet: 0.90 (0.35), residues: 218 loop : -0.43 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.020 0.002 PHE R 87 TYR 0.011 0.001 TYR R 303 ARG 0.004 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 1.039 Fit side-chains REVERT: A 29 GLN cc_start: 0.8229 (tp40) cc_final: 0.7917 (mm-40) REVERT: A 33 ASP cc_start: 0.7707 (p0) cc_final: 0.7457 (p0) REVERT: A 272 ASP cc_start: 0.7815 (m-30) cc_final: 0.7527 (m-30) REVERT: A 284 THR cc_start: 0.8744 (p) cc_final: 0.8328 (t) REVERT: A 381 ASP cc_start: 0.8257 (t0) cc_final: 0.7824 (t0) REVERT: B 59 TYR cc_start: 0.8772 (OUTLIER) cc_final: 0.8438 (m-80) REVERT: B 197 ARG cc_start: 0.7930 (mmm-85) cc_final: 0.7452 (mtp180) REVERT: B 214 ARG cc_start: 0.7898 (mpt-90) cc_final: 0.7380 (mpt-90) REVERT: B 217 MET cc_start: 0.8596 (ptm) cc_final: 0.8325 (ptm) REVERT: B 262 MET cc_start: 0.7997 (tpp) cc_final: 0.7613 (tpp) REVERT: B 335 PHE cc_start: 0.8844 (m-10) cc_final: 0.8522 (m-80) REVERT: G 46 LYS cc_start: 0.8412 (mtpt) cc_final: 0.8207 (mtpt) REVERT: N 28 THR cc_start: 0.8425 (OUTLIER) cc_final: 0.8215 (p) REVERT: N 29 PHE cc_start: 0.8609 (t80) cc_final: 0.8185 (t80) REVERT: R 65 MET cc_start: 0.7131 (tmm) cc_final: 0.6175 (tmm) REVERT: R 90 LEU cc_start: 0.7690 (tp) cc_final: 0.7377 (tm) REVERT: R 199 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7732 (ptt90) REVERT: R 318 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7448 (tt) REVERT: R 326 MET cc_start: 0.7732 (mmm) cc_final: 0.7384 (mmm) outliers start: 31 outliers final: 21 residues processed: 194 average time/residue: 1.3116 time to fit residues: 269.3447 Evaluate side-chains 201 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 119 PHE Chi-restraints excluded: chain R residue 122 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 199 ARG Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 318 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 96 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 4 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 0.2980 chunk 88 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 268 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.134933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.118196 restraints weight = 11599.222| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.07 r_work: 0.3425 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8528 Z= 0.183 Angle : 0.516 7.947 11559 Z= 0.269 Chirality : 0.041 0.139 1315 Planarity : 0.004 0.046 1458 Dihedral : 5.313 57.498 1277 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.31 % Allowed : 17.20 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.26), residues: 1033 helix: 2.01 (0.26), residues: 403 sheet: 0.84 (0.35), residues: 220 loop : -0.33 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.020 0.001 PHE R 87 TYR 0.009 0.001 TYR A 391 ARG 0.009 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 0.870 Fit side-chains REVERT: A 29 GLN cc_start: 0.8229 (tp40) cc_final: 0.7942 (mm-40) REVERT: A 33 ASP cc_start: 0.7720 (p0) cc_final: 0.7478 (p0) REVERT: A 272 ASP cc_start: 0.7846 (m-30) cc_final: 0.7541 (m-30) REVERT: A 284 THR cc_start: 0.8759 (p) cc_final: 0.8348 (t) REVERT: A 381 ASP cc_start: 0.8250 (t0) cc_final: 0.7828 (t0) REVERT: B 59 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.8360 (m-80) REVERT: B 197 ARG cc_start: 0.7930 (mmm-85) cc_final: 0.7422 (mtp180) REVERT: B 214 ARG cc_start: 0.7873 (mpt-90) cc_final: 0.7331 (mpt-90) REVERT: B 217 MET cc_start: 0.8577 (ptm) cc_final: 0.8306 (ptm) REVERT: B 246 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7665 (m-30) REVERT: B 262 MET cc_start: 0.7979 (tpp) cc_final: 0.7609 (tpp) REVERT: B 335 PHE cc_start: 0.8840 (m-10) cc_final: 0.8509 (m-80) REVERT: G 46 LYS cc_start: 0.8390 (mtpt) cc_final: 0.8183 (mtpt) REVERT: N 29 PHE cc_start: 0.8569 (t80) cc_final: 0.8123 (t80) REVERT: R 65 MET cc_start: 0.7129 (tmm) cc_final: 0.6147 (tmm) REVERT: R 199 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7705 (ptt90) REVERT: R 318 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7515 (tt) REVERT: R 326 MET cc_start: 0.7740 (mmm) cc_final: 0.7373 (mmm) outliers start: 30 outliers final: 23 residues processed: 191 average time/residue: 1.2912 time to fit residues: 261.1017 Evaluate side-chains 201 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 119 PHE Chi-restraints excluded: chain R residue 122 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 193 TRP Chi-restraints excluded: chain R residue 199 ARG Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 318 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 95 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 51 optimal weight: 0.0980 chunk 98 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.135959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.119402 restraints weight = 11491.058| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.04 r_work: 0.3440 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8528 Z= 0.170 Angle : 0.497 7.689 11559 Z= 0.263 Chirality : 0.041 0.139 1315 Planarity : 0.004 0.046 1458 Dihedral : 5.220 58.469 1277 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.98 % Allowed : 17.75 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.26), residues: 1033 helix: 2.07 (0.26), residues: 403 sheet: 0.90 (0.35), residues: 218 loop : -0.32 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.031 0.002 PHE R 309 TYR 0.009 0.001 TYR R 303 ARG 0.011 0.000 ARG A 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 0.931 Fit side-chains REVERT: A 29 GLN cc_start: 0.8209 (tp40) cc_final: 0.7920 (mm-40) REVERT: A 33 ASP cc_start: 0.7674 (p0) cc_final: 0.7428 (p0) REVERT: A 272 ASP cc_start: 0.7830 (m-30) cc_final: 0.7511 (m-30) REVERT: A 284 THR cc_start: 0.8776 (p) cc_final: 0.8364 (t) REVERT: A 381 ASP cc_start: 0.8240 (t0) cc_final: 0.7805 (t0) REVERT: B 59 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.8305 (m-80) REVERT: B 197 ARG cc_start: 0.7941 (mmm-85) cc_final: 0.7504 (mtp180) REVERT: B 214 ARG cc_start: 0.7899 (mpt-90) cc_final: 0.7427 (mpt-90) REVERT: B 217 MET cc_start: 0.8587 (ptm) cc_final: 0.8324 (ptm) REVERT: B 246 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7660 (m-30) REVERT: B 262 MET cc_start: 0.7970 (tpp) cc_final: 0.7614 (tpp) REVERT: B 335 PHE cc_start: 0.8818 (m-10) cc_final: 0.8479 (m-80) REVERT: G 46 LYS cc_start: 0.8408 (mtpt) cc_final: 0.8199 (mtpt) REVERT: N 29 PHE cc_start: 0.8556 (t80) cc_final: 0.8103 (t80) REVERT: N 110 VAL cc_start: 0.8470 (p) cc_final: 0.8241 (t) REVERT: R 65 MET cc_start: 0.7076 (tmm) cc_final: 0.6097 (tmm) REVERT: R 199 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7667 (ptt90) REVERT: R 201 THR cc_start: 0.8043 (t) cc_final: 0.7683 (p) REVERT: R 318 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7464 (tt) REVERT: R 326 MET cc_start: 0.7731 (mmm) cc_final: 0.7361 (mmm) outliers start: 27 outliers final: 22 residues processed: 186 average time/residue: 1.2624 time to fit residues: 249.0586 Evaluate side-chains 199 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 119 PHE Chi-restraints excluded: chain R residue 122 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 193 TRP Chi-restraints excluded: chain R residue 199 ARG Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 318 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 0.0070 chunk 84 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.136170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.119535 restraints weight = 11586.207| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.06 r_work: 0.3439 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8528 Z= 0.167 Angle : 0.507 7.812 11559 Z= 0.264 Chirality : 0.041 0.139 1315 Planarity : 0.004 0.045 1458 Dihedral : 5.160 59.402 1277 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.76 % Allowed : 18.30 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.26), residues: 1033 helix: 2.08 (0.26), residues: 403 sheet: 0.80 (0.35), residues: 220 loop : -0.29 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.028 0.001 PHE R 309 TYR 0.010 0.001 TYR A 391 ARG 0.011 0.000 ARG A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6745.91 seconds wall clock time: 119 minutes 45.38 seconds (7185.38 seconds total)