Starting phenix.real_space_refine on Mon Jul 28 08:49:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f9y_31500/07_2025/7f9y_31500_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f9y_31500/07_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_31500/07_2025/7f9y_31500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f9y_31500/07_2025/7f9y_31500.map" model { file = "/net/cci-nas-00/data/ceres_data/7f9y_31500/07_2025/7f9y_31500_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f9y_31500/07_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-5711/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: 5.47, per 1000 atoms: 0.65 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: 2.70 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.91 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: 2.41 Time building geometry restraints manager: 2.87 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: 0.000 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: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.310 Find NCS groups from input model: 0.070 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:13.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.000 ------------------------------------------------------------------------------- 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 8530 Z= 0.144 Angle : 0.552 8.573 11561 Z= 0.307 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 Details of bonding type rmsd hydrogen bonds : bond 0.17342 ( 412) hydrogen bonds : angle 6.13494 ( 1179) SS BOND : bond 0.00670 ( 1) SS BOND : angle 2.77898 ( 2) covalent geometry : bond 0.00267 ( 8528) covalent geometry : angle 0.55117 (11559) Misc. bond : bond 0.00010 ( 1) *********************** 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 : 0.864 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: 1.2577 time to fit residues: 271.3249 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 : 0.869 ------------------------------------------------------------------------------- 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: 2.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.3828 r_free = 0.3828 target = 0.139649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.122593 restraints weight = 11505.026| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.08 r_work: 0.3490 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8530 Z= 0.140 Angle : 0.569 7.728 11561 Z= 0.298 Chirality : 0.043 0.147 1315 Planarity : 0.004 0.053 1458 Dihedral : 5.851 59.676 1277 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.98 % Allowed : 9.81 % Favored : 88.20 % 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: 1.65 (0.27), residues: 1033 helix: 1.96 (0.26), residues: 401 sheet: 1.23 (0.34), residues: 221 loop : 0.24 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 47 HIS 0.007 0.001 HIS A 357 PHE 0.018 0.002 PHE R 279 TYR 0.014 0.001 TYR R 330 ARG 0.009 0.001 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04144 ( 412) hydrogen bonds : angle 4.51684 ( 1179) SS BOND : bond 0.00378 ( 1) SS BOND : angle 2.91527 ( 2) covalent geometry : bond 0.00315 ( 8528) covalent geometry : angle 0.56725 (11559) Misc. bond : bond 0.00011 ( 1) *********************** 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 199 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 1.020 Fit side-chains REVERT: A 29 GLN cc_start: 0.8180 (tp40) cc_final: 0.7940 (mm-40) REVERT: A 218 ASN cc_start: 0.8465 (m-40) cc_final: 0.8063 (m110) REVERT: A 266 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7635 (tt) REVERT: A 272 ASP cc_start: 0.7871 (m-30) cc_final: 0.7533 (m-30) REVERT: A 284 THR cc_start: 0.8597 (p) cc_final: 0.8154 (t) REVERT: A 381 ASP cc_start: 0.8272 (t0) cc_final: 0.7960 (t0) REVERT: A 390 GLU cc_start: 0.7255 (mm-30) cc_final: 0.7016 (mm-30) REVERT: A 391 TYR cc_start: 0.7378 (m-10) cc_final: 0.6905 (m-10) REVERT: B 29 THR cc_start: 0.8304 (OUTLIER) cc_final: 0.7908 (p) REVERT: B 197 ARG cc_start: 0.7650 (mmm-85) cc_final: 0.7313 (mmm-85) REVERT: B 214 ARG cc_start: 0.7661 (mpt-90) cc_final: 0.7208 (mpp80) REVERT: B 219 ARG cc_start: 0.8334 (mtt-85) cc_final: 0.8106 (mmm-85) REVERT: B 262 MET cc_start: 0.8187 (tpp) cc_final: 0.7740 (tpp) REVERT: G 47 GLU cc_start: 0.8179 (tt0) cc_final: 0.7909 (tt0) REVERT: N 29 PHE cc_start: 0.8454 (t80) cc_final: 0.8129 (t80) REVERT: R 65 MET cc_start: 0.7050 (tmm) cc_final: 0.6075 (tmm) REVERT: R 201 THR cc_start: 0.7959 (t) cc_final: 0.7631 (p) REVERT: R 213 MET cc_start: 0.7048 (mtp) cc_final: 0.6551 (mtm) REVERT: R 326 MET cc_start: 0.7732 (mmm) cc_final: 0.7469 (mmm) outliers start: 18 outliers final: 9 residues processed: 190 average time/residue: 1.2299 time to fit residues: 248.6315 Evaluate side-chains 189 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 178 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 266 LEU 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 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: 0.9980 chunk 76 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 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 268 ASN B 340 ASN N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.136598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.119147 restraints weight = 11608.440| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.06 r_work: 0.3432 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8530 Z= 0.153 Angle : 0.546 8.336 11561 Z= 0.286 Chirality : 0.043 0.143 1315 Planarity : 0.004 0.048 1458 Dihedral : 5.609 48.421 1277 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.09 % Allowed : 12.24 % Favored : 84.67 % 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: 1.46 (0.26), residues: 1033 helix: 1.89 (0.26), residues: 396 sheet: 1.13 (0.35), residues: 213 loop : 0.08 (0.30), residues: 424 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 0.023 0.002 PHE R 312 TYR 0.014 0.001 TYR B 59 ARG 0.011 0.001 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04112 ( 412) hydrogen bonds : angle 4.28348 ( 1179) SS BOND : bond 0.00368 ( 1) SS BOND : angle 2.58956 ( 2) covalent geometry : bond 0.00351 ( 8528) covalent geometry : angle 0.54475 (11559) Misc. bond : bond 0.00030 ( 1) *********************** 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 221 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 0.860 Fit side-chains REVERT: A 29 GLN cc_start: 0.8273 (tp40) cc_final: 0.8011 (mm-40) REVERT: A 272 ASP cc_start: 0.7885 (m-30) cc_final: 0.7600 (m-30) REVERT: A 283 ARG cc_start: 0.7998 (mtm110) cc_final: 0.7712 (mtm-85) REVERT: A 284 THR cc_start: 0.8568 (p) cc_final: 0.8124 (t) REVERT: A 381 ASP cc_start: 0.8327 (t0) cc_final: 0.7984 (t0) REVERT: B 197 ARG cc_start: 0.7883 (mmm-85) cc_final: 0.7585 (mmm-85) REVERT: B 214 ARG cc_start: 0.7832 (mpt-90) cc_final: 0.7485 (mmm-85) REVERT: B 217 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8268 (ptm) REVERT: B 219 ARG cc_start: 0.8426 (mtt-85) cc_final: 0.8172 (mmm-85) REVERT: B 262 MET cc_start: 0.8135 (tpp) cc_final: 0.7708 (tpp) REVERT: B 335 PHE cc_start: 0.8864 (m-10) cc_final: 0.8441 (m-80) REVERT: G 46 LYS cc_start: 0.8392 (mtpt) cc_final: 0.8190 (mtpt) REVERT: G 47 GLU cc_start: 0.8289 (tt0) cc_final: 0.8040 (tt0) REVERT: N 29 PHE cc_start: 0.8610 (t80) cc_final: 0.8185 (t80) REVERT: R 65 MET cc_start: 0.7164 (tmm) cc_final: 0.6183 (tmm) REVERT: R 91 LEU cc_start: 0.7889 (tt) cc_final: 0.7619 (tp) REVERT: R 199 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7767 (ptt90) REVERT: R 201 THR cc_start: 0.8087 (t) cc_final: 0.7720 (p) REVERT: R 213 MET cc_start: 0.7159 (mtp) cc_final: 0.6772 (mtm) REVERT: R 216 VAL cc_start: 0.8346 (t) cc_final: 0.8101 (p) REVERT: R 270 PHE cc_start: 0.7486 (t80) cc_final: 0.7269 (t80) REVERT: R 326 MET cc_start: 0.7716 (mmm) cc_final: 0.7410 (mmm) outliers start: 28 outliers final: 12 residues processed: 205 average time/residue: 1.1752 time to fit residues: 256.0446 Evaluate side-chains 204 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 190 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 143 THR Chi-restraints excluded: chain B residue 217 MET 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: 0.7980 chunk 26 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 13 optimal weight: 0.0170 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 83 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.136867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.120029 restraints weight = 11533.124| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.06 r_work: 0.3446 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8530 Z= 0.125 Angle : 0.506 7.530 11561 Z= 0.267 Chirality : 0.041 0.139 1315 Planarity : 0.004 0.044 1458 Dihedral : 5.408 48.254 1277 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.20 % Allowed : 14.44 % Favored : 82.36 % 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: 1.39 (0.26), residues: 1033 helix: 1.89 (0.26), residues: 405 sheet: 1.10 (0.35), residues: 213 loop : -0.09 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.022 0.002 PHE R 309 TYR 0.012 0.001 TYR R 330 ARG 0.008 0.000 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 412) hydrogen bonds : angle 4.10662 ( 1179) SS BOND : bond 0.00202 ( 1) SS BOND : angle 2.64182 ( 2) covalent geometry : bond 0.00283 ( 8528) covalent geometry : angle 0.50467 (11559) Misc. bond : bond 0.00031 ( 1) *********************** 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 216 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8236 (tp40) cc_final: 0.7932 (mm-40) REVERT: A 33 ASP cc_start: 0.7628 (p0) cc_final: 0.7363 (p0) REVERT: A 40 THR cc_start: 0.8131 (OUTLIER) cc_final: 0.7898 (m) REVERT: A 272 ASP cc_start: 0.7833 (m-30) cc_final: 0.7509 (m-30) REVERT: A 283 ARG cc_start: 0.7955 (mtm110) cc_final: 0.7644 (mtm-85) REVERT: A 284 THR cc_start: 0.8667 (p) cc_final: 0.8218 (t) REVERT: A 381 ASP cc_start: 0.8263 (t0) cc_final: 0.7806 (t0) REVERT: B 96 ARG cc_start: 0.8339 (ttm-80) cc_final: 0.8094 (ttm170) REVERT: B 188 MET cc_start: 0.8229 (mmm) cc_final: 0.8021 (mmp) REVERT: B 219 ARG cc_start: 0.8402 (mtt-85) cc_final: 0.8161 (mmm-85) REVERT: B 262 MET cc_start: 0.8107 (tpp) cc_final: 0.7666 (tpp) REVERT: B 335 PHE cc_start: 0.8834 (m-10) cc_final: 0.8485 (m-80) REVERT: G 46 LYS cc_start: 0.8350 (mtpt) cc_final: 0.8143 (mtpt) REVERT: G 47 GLU cc_start: 0.8203 (tt0) cc_final: 0.7947 (tt0) REVERT: N 29 PHE cc_start: 0.8582 (t80) cc_final: 0.8166 (t80) REVERT: R 65 MET cc_start: 0.7099 (tmm) cc_final: 0.6146 (tmm) REVERT: R 91 LEU cc_start: 0.7746 (tt) cc_final: 0.7540 (tp) REVERT: R 199 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7655 (ptt90) REVERT: R 201 THR cc_start: 0.8031 (t) cc_final: 0.7663 (p) REVERT: R 213 MET cc_start: 0.7150 (mtp) cc_final: 0.6799 (mtm) REVERT: R 216 VAL cc_start: 0.8330 (t) cc_final: 0.8081 (p) REVERT: R 326 MET cc_start: 0.7751 (mmm) cc_final: 0.7404 (mmm) outliers start: 29 outliers final: 13 residues processed: 200 average time/residue: 1.1644 time to fit residues: 247.9815 Evaluate side-chains 192 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 177 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 322 GLU 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 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 111 THR Chi-restraints excluded: chain R residue 119 PHE Chi-restraints excluded: chain R residue 122 VAL Chi-restraints excluded: chain R residue 199 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 86 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 C 12 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.134217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.117374 restraints weight = 11434.281| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.05 r_work: 0.3387 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8530 Z= 0.195 Angle : 0.556 7.228 11561 Z= 0.292 Chirality : 0.043 0.143 1315 Planarity : 0.004 0.046 1458 Dihedral : 5.640 51.767 1277 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.97 % Allowed : 14.33 % Favored : 81.70 % 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: 1.12 (0.26), residues: 1033 helix: 1.71 (0.26), residues: 409 sheet: 1.03 (0.35), residues: 213 loop : -0.36 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.024 0.002 PHE R 312 TYR 0.015 0.002 TYR R 81 ARG 0.005 0.000 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.04217 ( 412) hydrogen bonds : angle 4.22938 ( 1179) SS BOND : bond 0.00477 ( 1) SS BOND : angle 2.63933 ( 2) covalent geometry : bond 0.00456 ( 8528) covalent geometry : angle 0.55468 (11559) Misc. bond : bond 0.00068 ( 1) *********************** 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 213 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8214 (tp40) cc_final: 0.7914 (mm-40) REVERT: A 33 ASP cc_start: 0.7640 (p0) cc_final: 0.7418 (p0) REVERT: A 272 ASP cc_start: 0.7802 (m-30) cc_final: 0.7497 (m-30) REVERT: A 283 ARG cc_start: 0.7944 (mtm110) cc_final: 0.7688 (ttp-110) REVERT: A 284 THR cc_start: 0.8670 (p) cc_final: 0.8205 (t) REVERT: A 342 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7359 (ttm110) REVERT: A 381 ASP cc_start: 0.8258 (t0) cc_final: 0.7816 (t0) REVERT: B 138 GLU cc_start: 0.7839 (pt0) cc_final: 0.7638 (pp20) REVERT: B 262 MET cc_start: 0.8086 (tpp) cc_final: 0.7656 (tpp) REVERT: B 335 PHE cc_start: 0.8866 (m-10) cc_final: 0.8472 (m-80) REVERT: G 46 LYS cc_start: 0.8420 (mtpt) cc_final: 0.8214 (mtpt) REVERT: G 47 GLU cc_start: 0.8224 (tt0) cc_final: 0.8007 (tt0) REVERT: N 28 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.8116 (p) REVERT: N 29 PHE cc_start: 0.8631 (t80) cc_final: 0.8206 (t80) REVERT: R 65 MET cc_start: 0.7155 (tmm) cc_final: 0.6201 (tmm) REVERT: R 199 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7824 (ptt90) REVERT: R 213 MET cc_start: 0.7238 (mtp) cc_final: 0.6897 (mtm) REVERT: R 216 VAL cc_start: 0.8318 (t) cc_final: 0.8080 (p) REVERT: R 326 MET cc_start: 0.7774 (mmm) cc_final: 0.7423 (mmm) outliers start: 36 outliers final: 21 residues processed: 193 average time/residue: 1.1703 time to fit residues: 240.3512 Evaluate side-chains 197 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 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 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 119 PHE Chi-restraints excluded: chain R residue 180 VAL 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: 0.9980 chunk 58 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 0.2980 chunk 26 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.135020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.118277 restraints weight = 11412.904| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.05 r_work: 0.3407 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8530 Z= 0.144 Angle : 0.515 7.616 11561 Z= 0.271 Chirality : 0.042 0.140 1315 Planarity : 0.004 0.047 1458 Dihedral : 5.502 53.658 1277 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.19 % Allowed : 15.33 % 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: 1.20 (0.26), residues: 1033 helix: 1.88 (0.26), residues: 403 sheet: 0.90 (0.35), residues: 219 loop : -0.30 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 47 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.002 PHE R 119 TYR 0.010 0.001 TYR R 330 ARG 0.006 0.000 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 412) hydrogen bonds : angle 4.11884 ( 1179) SS BOND : bond 0.00258 ( 1) SS BOND : angle 2.64766 ( 2) covalent geometry : bond 0.00330 ( 8528) covalent geometry : angle 0.51408 (11559) Misc. bond : bond 0.00040 ( 1) *********************** 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 215 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8229 (tp40) cc_final: 0.7917 (mm-40) REVERT: A 33 ASP cc_start: 0.7632 (p0) cc_final: 0.7383 (p0) REVERT: A 272 ASP cc_start: 0.7817 (m-30) cc_final: 0.7513 (m-30) REVERT: A 283 ARG cc_start: 0.7945 (mtm110) cc_final: 0.7684 (ttp-110) REVERT: A 284 THR cc_start: 0.8692 (p) cc_final: 0.8244 (t) REVERT: A 381 ASP cc_start: 0.8261 (t0) cc_final: 0.7836 (t0) REVERT: B 138 GLU cc_start: 0.7853 (pt0) cc_final: 0.7639 (pp20) REVERT: B 217 MET cc_start: 0.8604 (ptm) cc_final: 0.8353 (ptm) REVERT: B 262 MET cc_start: 0.8075 (tpp) cc_final: 0.7655 (tpp) REVERT: B 335 PHE cc_start: 0.8855 (m-10) cc_final: 0.8491 (m-80) REVERT: G 46 LYS cc_start: 0.8410 (mtpt) cc_final: 0.8205 (mtpt) REVERT: N 28 THR cc_start: 0.8315 (OUTLIER) cc_final: 0.8047 (p) REVERT: N 29 PHE cc_start: 0.8636 (t80) cc_final: 0.8191 (t80) REVERT: R 65 MET cc_start: 0.7168 (tmm) cc_final: 0.6217 (tmm) REVERT: R 199 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7744 (ptt90) REVERT: R 213 MET cc_start: 0.7224 (mtp) cc_final: 0.6912 (mtm) REVERT: R 216 VAL cc_start: 0.8345 (t) cc_final: 0.8093 (p) REVERT: R 318 ILE cc_start: 0.7790 (OUTLIER) cc_final: 0.7487 (tt) REVERT: R 326 MET cc_start: 0.7751 (mmm) cc_final: 0.7410 (mmm) outliers start: 38 outliers final: 25 residues processed: 194 average time/residue: 1.2409 time to fit residues: 255.1839 Evaluate side-chains 204 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR 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 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 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 155 VAL Chi-restraints excluded: chain R residue 199 ARG Chi-restraints excluded: chain R residue 267 VAL 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: 1.9990 chunk 98 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.135165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.118507 restraints weight = 11480.300| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.04 r_work: 0.3423 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8530 Z= 0.137 Angle : 0.511 7.559 11561 Z= 0.269 Chirality : 0.042 0.141 1315 Planarity : 0.004 0.046 1458 Dihedral : 5.425 55.332 1277 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.53 % Allowed : 16.21 % Favored : 80.26 % 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: 1.24 (0.26), residues: 1033 helix: 1.94 (0.26), residues: 403 sheet: 0.94 (0.35), residues: 219 loop : -0.33 (0.31), residues: 411 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 0.010 0.001 TYR R 303 ARG 0.007 0.000 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.03793 ( 412) hydrogen bonds : angle 4.04608 ( 1179) SS BOND : bond 0.00330 ( 1) SS BOND : angle 2.44697 ( 2) covalent geometry : bond 0.00312 ( 8528) covalent geometry : angle 0.50966 (11559) Misc. bond : bond 0.00035 ( 1) *********************** 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 212 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8226 (tp40) cc_final: 0.7944 (mm-40) REVERT: A 33 ASP cc_start: 0.7666 (p0) cc_final: 0.7414 (p0) REVERT: A 53 LYS cc_start: 0.7958 (ptmt) cc_final: 0.7722 (pttt) REVERT: A 272 ASP cc_start: 0.7798 (m-30) cc_final: 0.7513 (m-30) REVERT: A 283 ARG cc_start: 0.7912 (mtm110) cc_final: 0.7661 (ttp-110) REVERT: A 284 THR cc_start: 0.8692 (p) cc_final: 0.8247 (t) REVERT: A 381 ASP cc_start: 0.8246 (t0) cc_final: 0.7817 (t0) REVERT: B 59 TYR cc_start: 0.8774 (OUTLIER) cc_final: 0.8402 (m-80) REVERT: B 138 GLU cc_start: 0.7832 (pt0) cc_final: 0.7628 (pp20) REVERT: B 197 ARG cc_start: 0.7983 (mmm-85) cc_final: 0.7706 (mtp180) REVERT: B 217 MET cc_start: 0.8595 (ptm) cc_final: 0.8321 (ptm) REVERT: B 262 MET cc_start: 0.8027 (tpp) cc_final: 0.7623 (tpp) REVERT: B 335 PHE cc_start: 0.8840 (m-10) cc_final: 0.8530 (m-80) REVERT: G 46 LYS cc_start: 0.8420 (mtpt) cc_final: 0.8218 (mtpt) REVERT: N 28 THR cc_start: 0.8297 (OUTLIER) cc_final: 0.8036 (p) REVERT: N 29 PHE cc_start: 0.8620 (t80) cc_final: 0.8217 (t80) REVERT: N 38 ARG cc_start: 0.8832 (ptt180) cc_final: 0.8588 (ptt180) REVERT: R 65 MET cc_start: 0.7152 (tmm) cc_final: 0.6193 (tmm) REVERT: R 90 LEU cc_start: 0.7696 (tp) cc_final: 0.7385 (tm) REVERT: R 102 ARG cc_start: 0.8477 (ttp-170) cc_final: 0.8229 (ttp-170) REVERT: R 199 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7691 (ptt90) REVERT: R 201 THR cc_start: 0.8058 (t) cc_final: 0.7697 (p) REVERT: R 318 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7454 (tt) REVERT: R 326 MET cc_start: 0.7744 (mmm) cc_final: 0.7397 (mmm) outliers start: 32 outliers final: 19 residues processed: 197 average time/residue: 1.2246 time to fit residues: 255.9562 Evaluate side-chains 201 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR 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 37 ILE 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 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 199 ARG Chi-restraints excluded: chain R residue 318 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 21 optimal weight: 0.6980 chunk 76 optimal weight: 7.9990 chunk 72 optimal weight: 0.1980 chunk 66 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.135111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.118306 restraints weight = 11580.429| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.07 r_work: 0.3432 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8530 Z= 0.128 Angle : 0.506 8.339 11561 Z= 0.265 Chirality : 0.041 0.139 1315 Planarity : 0.004 0.046 1458 Dihedral : 5.337 56.792 1277 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.31 % Allowed : 17.09 % 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: 1.16 (0.26), residues: 1033 helix: 1.90 (0.26), residues: 409 sheet: 0.85 (0.35), residues: 220 loop : -0.42 (0.30), residues: 404 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 0.002 PHE R 87 TYR 0.010 0.001 TYR R 303 ARG 0.007 0.000 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 412) hydrogen bonds : angle 3.99702 ( 1179) SS BOND : bond 0.00454 ( 1) SS BOND : angle 2.47839 ( 2) covalent geometry : bond 0.00291 ( 8528) covalent geometry : angle 0.50502 (11559) Misc. bond : bond 0.00037 ( 1) *********************** 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 204 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8225 (tp40) cc_final: 0.7941 (mm-40) REVERT: A 33 ASP cc_start: 0.7614 (p0) cc_final: 0.7345 (p0) REVERT: A 53 LYS cc_start: 0.7918 (ptmt) cc_final: 0.7686 (pttt) REVERT: A 272 ASP cc_start: 0.7836 (m-30) cc_final: 0.7516 (m-30) REVERT: A 283 ARG cc_start: 0.7916 (mtm110) cc_final: 0.7669 (ttp-110) REVERT: A 284 THR cc_start: 0.8681 (p) cc_final: 0.8245 (t) REVERT: A 381 ASP cc_start: 0.8224 (t0) cc_final: 0.7790 (t0) REVERT: B 59 TYR cc_start: 0.8776 (OUTLIER) cc_final: 0.8414 (m-80) REVERT: B 138 GLU cc_start: 0.7861 (pt0) cc_final: 0.7652 (pp20) REVERT: B 197 ARG cc_start: 0.7963 (mmm-85) cc_final: 0.7692 (mtp180) REVERT: B 217 MET cc_start: 0.8589 (ptm) cc_final: 0.8316 (ptm) REVERT: B 262 MET cc_start: 0.8005 (tpp) cc_final: 0.7624 (tpp) REVERT: B 335 PHE cc_start: 0.8830 (m-10) cc_final: 0.8509 (m-80) REVERT: N 28 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.8013 (p) REVERT: N 29 PHE cc_start: 0.8623 (t80) cc_final: 0.8243 (t80) REVERT: R 65 MET cc_start: 0.7120 (tmm) cc_final: 0.6139 (tmm) REVERT: R 199 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.6809 (ppp80) REVERT: R 201 THR cc_start: 0.8058 (t) cc_final: 0.7736 (p) REVERT: R 318 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7489 (tt) REVERT: R 326 MET cc_start: 0.7761 (mmm) cc_final: 0.7383 (mmm) outliers start: 30 outliers final: 21 residues processed: 189 average time/residue: 1.2525 time to fit residues: 251.1834 Evaluate side-chains 197 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR 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 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 45 MET 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 270 ILE 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 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 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: 0.6980 chunk 60 optimal weight: 0.0050 chunk 18 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 65 optimal weight: 0.0770 chunk 63 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.4352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 239 ASN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.136080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.119257 restraints weight = 11575.007| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.08 r_work: 0.3440 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 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 : 0.002 0.028 8530 Z= 0.106 Angle : 0.484 7.778 11561 Z= 0.256 Chirality : 0.040 0.139 1315 Planarity : 0.004 0.045 1458 Dihedral : 5.175 57.754 1277 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.76 % Allowed : 17.53 % Favored : 79.71 % 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: 1.43 (0.27), residues: 1033 helix: 2.21 (0.26), residues: 397 sheet: 0.88 (0.35), residues: 221 loop : -0.22 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.019 0.001 PHE R 87 TYR 0.009 0.001 TYR B 111 ARG 0.007 0.000 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.03449 ( 412) hydrogen bonds : angle 3.90264 ( 1179) SS BOND : bond 0.00359 ( 1) SS BOND : angle 2.35304 ( 2) covalent geometry : bond 0.00233 ( 8528) covalent geometry : angle 0.48295 (11559) Misc. bond : bond 0.00023 ( 1) *********************** 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 201 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.998 Fit side-chains REVERT: A 29 GLN cc_start: 0.8224 (tp40) cc_final: 0.7936 (mm-40) REVERT: A 33 ASP cc_start: 0.7626 (p0) cc_final: 0.7348 (p0) REVERT: A 272 ASP cc_start: 0.7834 (m-30) cc_final: 0.7506 (m-30) REVERT: A 283 ARG cc_start: 0.7912 (mtm110) cc_final: 0.7661 (ttp-110) REVERT: A 284 THR cc_start: 0.8697 (p) cc_final: 0.8257 (t) REVERT: A 374 ARG cc_start: 0.8483 (mtt90) cc_final: 0.8270 (mtt180) REVERT: A 381 ASP cc_start: 0.8224 (t0) cc_final: 0.7788 (t0) REVERT: B 114 CYS cc_start: 0.8261 (p) cc_final: 0.8011 (p) REVERT: B 138 GLU cc_start: 0.7845 (pt0) cc_final: 0.7641 (pp20) REVERT: B 188 MET cc_start: 0.8246 (mmm) cc_final: 0.8045 (mmp) REVERT: B 197 ARG cc_start: 0.7981 (mmm-85) cc_final: 0.7423 (mtp180) REVERT: B 214 ARG cc_start: 0.7894 (mpt-90) cc_final: 0.7218 (mmm-85) REVERT: B 217 MET cc_start: 0.8564 (ptm) cc_final: 0.8281 (ptm) REVERT: B 239 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.8020 (m-40) REVERT: B 246 ASP cc_start: 0.7906 (m-30) cc_final: 0.7651 (m-30) REVERT: B 262 MET cc_start: 0.7988 (tpp) cc_final: 0.7638 (tpp) REVERT: B 335 PHE cc_start: 0.8817 (m-10) cc_final: 0.8486 (m-80) REVERT: N 28 THR cc_start: 0.8261 (OUTLIER) cc_final: 0.7982 (p) REVERT: N 110 VAL cc_start: 0.8398 (p) cc_final: 0.8177 (t) REVERT: R 65 MET cc_start: 0.7049 (tmm) cc_final: 0.6071 (tmm) REVERT: R 199 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7692 (ptt90) REVERT: R 201 THR cc_start: 0.8027 (t) cc_final: 0.7671 (p) REVERT: R 318 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7462 (tt) REVERT: R 326 MET cc_start: 0.7750 (mmm) cc_final: 0.7386 (mmm) outliers start: 25 outliers final: 15 residues processed: 187 average time/residue: 1.2561 time to fit residues: 249.2672 Evaluate side-chains 193 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS 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 45 MET 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 239 ASN 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 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 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: 0.4980 chunk 30 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.135443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.118738 restraints weight = 11495.849| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.06 r_work: 0.3434 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8530 Z= 0.145 Angle : 0.513 7.895 11561 Z= 0.270 Chirality : 0.042 0.143 1315 Planarity : 0.004 0.061 1458 Dihedral : 5.247 58.367 1277 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.54 % Allowed : 17.86 % 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: 1.25 (0.26), residues: 1033 helix: 1.96 (0.26), residues: 409 sheet: 0.85 (0.35), residues: 220 loop : -0.32 (0.31), residues: 404 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 0.021 0.002 PHE R 87 TYR 0.011 0.001 TYR R 303 ARG 0.009 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.03689 ( 412) hydrogen bonds : angle 3.95029 ( 1179) SS BOND : bond 0.00343 ( 1) SS BOND : angle 2.64039 ( 2) covalent geometry : bond 0.00335 ( 8528) covalent geometry : angle 0.51207 (11559) Misc. bond : bond 0.00043 ( 1) ********************** 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 196 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.876 Fit side-chains REVERT: A 29 GLN cc_start: 0.8224 (tp40) cc_final: 0.7945 (mm-40) REVERT: A 33 ASP cc_start: 0.7608 (p0) cc_final: 0.7356 (p0) REVERT: A 272 ASP cc_start: 0.7843 (m-30) cc_final: 0.7530 (m-30) REVERT: A 283 ARG cc_start: 0.7933 (mtm110) cc_final: 0.7680 (ttp-110) REVERT: A 284 THR cc_start: 0.8699 (p) cc_final: 0.8260 (t) REVERT: A 381 ASP cc_start: 0.8228 (t0) cc_final: 0.7788 (t0) REVERT: B 197 ARG cc_start: 0.7967 (mmm-85) cc_final: 0.7176 (mtp180) REVERT: B 214 ARG cc_start: 0.7901 (mpt-90) cc_final: 0.7004 (mmt90) REVERT: B 217 MET cc_start: 0.8559 (ptm) cc_final: 0.8280 (ptm) REVERT: B 262 MET cc_start: 0.7985 (tpp) cc_final: 0.7618 (tpp) REVERT: B 335 PHE cc_start: 0.8833 (m-10) cc_final: 0.8501 (m-80) REVERT: N 28 THR cc_start: 0.8279 (OUTLIER) cc_final: 0.8025 (p) REVERT: R 65 MET cc_start: 0.7057 (tmm) cc_final: 0.6070 (tmm) REVERT: R 199 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.6825 (ppp80) REVERT: R 201 THR cc_start: 0.8061 (t) cc_final: 0.7726 (p) REVERT: R 318 ILE cc_start: 0.7787 (OUTLIER) cc_final: 0.7503 (tt) REVERT: R 326 MET cc_start: 0.7678 (mmm) cc_final: 0.7308 (mmm) outliers start: 23 outliers final: 17 residues processed: 182 average time/residue: 1.3214 time to fit residues: 255.0919 Evaluate side-chains 190 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS 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 45 MET 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 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 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: 3.9990 chunk 84 optimal weight: 0.0050 chunk 59 optimal weight: 0.0170 chunk 4 optimal weight: 0.6980 chunk 99 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.4032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 239 ASN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.136855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.120196 restraints weight = 11599.212| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.07 r_work: 0.3452 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8530 Z= 0.105 Angle : 0.490 7.843 11561 Z= 0.257 Chirality : 0.040 0.139 1315 Planarity : 0.004 0.060 1458 Dihedral : 5.105 59.392 1277 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.65 % Allowed : 18.30 % Favored : 79.05 % 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: 1.51 (0.26), residues: 1033 helix: 2.25 (0.26), residues: 397 sheet: 0.94 (0.34), residues: 219 loop : -0.16 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.020 0.001 PHE R 87 TYR 0.009 0.001 TYR B 111 ARG 0.011 0.000 ARG A 39 Details of bonding type rmsd hydrogen bonds : bond 0.03383 ( 412) hydrogen bonds : angle 3.87193 ( 1179) SS BOND : bond 0.00313 ( 1) SS BOND : angle 2.41599 ( 2) covalent geometry : bond 0.00231 ( 8528) covalent geometry : angle 0.48940 (11559) Misc. bond : bond 0.00027 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6901.10 seconds wall clock time: 118 minutes 44.88 seconds (7124.88 seconds total)