Starting phenix.real_space_refine on Fri Sep 11 12:23:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xbm_22120/09_2026/6xbm_22120.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xbm_22120/09_2026/6xbm_22120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xbm_22120/09_2026/6xbm_22120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xbm_22120/09_2026/6xbm_22120.map" model { file = "/net/cci-nas-00/data/ceres_data/6xbm_22120/09_2026/6xbm_22120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xbm_22120/09_2026/6xbm_22120.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6xbm_22120/09_2026/6xbm_22120.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xbm_22120/09_2026/6xbm_22120.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 5880 2.51 5 N 1543 2.21 5 O 1724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9211 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2618 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 10, 'TRANS': 320} Chain breaks: 1 Chain: "A" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1736 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 2 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "S" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1785 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'CO1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.99, per 1000 atoms: 0.22 Number of scatterers: 9211 At special positions: 0 Unit cell: (105.664, 112.32, 126.464, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 1724 8.00 N 1543 7.00 C 5880 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 193 " - pdb=" SG CYS R 213 " distance=2.03 Simple disulfide: pdb=" SG CYS R 217 " - pdb=" SG CYS R 295 " distance=2.03 Simple disulfide: pdb=" SG CYS R 314 " - pdb=" SG CYS R 390 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.02 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 374.3 milliseconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2166 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 14 sheets defined 36.2% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'R' and resid 223 through 254 Processing helix chain 'R' and resid 261 through 283 removed outlier: 3.693A pdb=" N ILE R 266 " --> pdb=" O TYR R 262 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LEU R 267 " --> pdb=" O PRO R 263 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE R 268 " --> pdb=" O ALA R 264 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 295 Processing helix chain 'R' and resid 312 through 345 removed outlier: 3.557A pdb=" N ALA R 345 " --> pdb=" O THR R 341 " (cutoff:3.500A) Processing helix chain 'R' and resid 356 through 379 Proline residue: R 368 - end of helix Processing helix chain 'R' and resid 396 through 433 removed outlier: 3.959A pdb=" N ARG R 400 " --> pdb=" O ASN R 396 " (cutoff:3.500A) Proline residue: R 407 - end of helix removed outlier: 4.262A pdb=" N LYS R 430 " --> pdb=" O LEU R 426 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N SER R 431 " --> pdb=" O PHE R 427 " (cutoff:3.500A) Processing helix chain 'R' and resid 438 through 496 removed outlier: 4.483A pdb=" N ALA R 478 " --> pdb=" O PHE R 474 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU R 479 " --> pdb=" O PHE R 475 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG R 482 " --> pdb=" O ALA R 478 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG R 485 " --> pdb=" O GLU R 481 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN R 491 " --> pdb=" O TYR R 487 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE R 496 " --> pdb=" O ALA R 492 " (cutoff:3.500A) Processing helix chain 'R' and resid 514 through 534 removed outlier: 4.434A pdb=" N GLU R 518 " --> pdb=" O SER R 514 " (cutoff:3.500A) Processing helix chain 'R' and resid 535 through 537 No H-bonds generated for 'chain 'R' and resid 535 through 537' Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.720A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.640A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.535A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 255 removed outlier: 3.504A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.139A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.716A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.786A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.877A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.770A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'R' and resid 381 through 383 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.755A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 51 Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.983A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.892A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.645A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.593A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.766A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 275 through 278 removed outlier: 6.519A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 315 through 317 removed outlier: 6.612A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.557A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.725A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 446 hydrogen bonds defined for protein. 1263 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: 1.72 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1925 1.33 - 1.45: 2224 1.45 - 1.58: 5160 1.58 - 1.70: 19 1.70 - 1.82: 92 Bond restraints: 9420 Sorted by residual: bond pdb=" C14 CO1 R 702 " pdb=" C7 CO1 R 702 " ideal model delta sigma weight residual 1.519 1.632 -0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" C14 CO1 R 701 " pdb=" C7 CO1 R 701 " ideal model delta sigma weight residual 1.519 1.626 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" N ILE B 270 " pdb=" CA ILE B 270 " ideal model delta sigma weight residual 1.457 1.496 -0.039 9.30e-03 1.16e+04 1.77e+01 bond pdb=" N ILE B 93 " pdb=" CA ILE B 93 " ideal model delta sigma weight residual 1.460 1.492 -0.032 7.60e-03 1.73e+04 1.75e+01 bond pdb=" C10 CO1 R 701 " pdb=" C17 CO1 R 701 " ideal model delta sigma weight residual 1.535 1.619 -0.084 2.00e-02 2.50e+03 1.74e+01 ... (remaining 9415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 9011 1.86 - 3.71: 3457 3.71 - 5.57: 296 5.57 - 7.42: 10 7.42 - 9.28: 3 Bond angle restraints: 12777 Sorted by residual: angle pdb=" C GLU R 194 " pdb=" N VAL R 195 " pdb=" CA VAL R 195 " ideal model delta sigma weight residual 120.33 125.40 -5.07 8.00e-01 1.56e+00 4.02e+01 angle pdb=" C PHE R 526 " pdb=" N GLY R 527 " pdb=" CA GLY R 527 " ideal model delta sigma weight residual 119.98 124.88 -4.90 1.11e+00 8.12e-01 1.95e+01 angle pdb=" CA ASP A 229 " pdb=" CB ASP A 229 " pdb=" CG ASP A 229 " ideal model delta sigma weight residual 112.60 116.90 -4.30 1.00e+00 1.00e+00 1.85e+01 angle pdb=" CA THR R 466 " pdb=" CB THR R 466 " pdb=" OG1 THR R 466 " ideal model delta sigma weight residual 109.60 103.23 6.37 1.50e+00 4.44e-01 1.81e+01 angle pdb=" C THR A 295 " pdb=" N TYR A 296 " pdb=" CA TYR A 296 " ideal model delta sigma weight residual 120.44 125.88 -5.44 1.30e+00 5.92e-01 1.75e+01 ... (remaining 12772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 4960 16.81 - 33.62: 441 33.62 - 50.42: 88 50.42 - 67.23: 21 67.23 - 84.04: 9 Dihedral angle restraints: 5519 sinusoidal: 2148 harmonic: 3371 Sorted by residual: dihedral pdb=" CA TYR S 223 " pdb=" C TYR S 223 " pdb=" N PRO S 224 " pdb=" CA PRO S 224 " ideal model delta harmonic sigma weight residual 180.00 122.21 57.79 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CB CYS R 193 " pdb=" SG CYS R 193 " pdb=" SG CYS R 213 " pdb=" CB CYS R 213 " ideal model delta sinusoidal sigma weight residual 93.00 172.76 -79.76 1 1.00e+01 1.00e-02 7.89e+01 dihedral pdb=" CA GLU R 305 " pdb=" C GLU R 305 " pdb=" N PRO R 306 " pdb=" CA PRO R 306 " ideal model delta harmonic sigma weight residual 180.00 140.97 39.03 0 5.00e+00 4.00e-02 6.09e+01 ... (remaining 5516 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1037 0.091 - 0.182: 377 0.182 - 0.273: 12 0.273 - 0.364: 1 0.364 - 0.455: 6 Chirality restraints: 1433 Sorted by residual: chirality pdb=" C2 CO1 R 701 " pdb=" C1 CO1 R 701 " pdb=" C5 CO1 R 701 " pdb=" C6 CO1 R 701 " both_signs ideal model delta sigma weight residual False -2.32 -2.78 0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" C7 CO1 R 702 " pdb=" C14 CO1 R 702 " pdb=" C15 CO1 R 702 " pdb=" C3 CO1 R 702 " both_signs ideal model delta sigma weight residual False 2.86 3.31 -0.45 2.00e-01 2.50e+01 5.12e+00 chirality pdb=" C2 CO1 R 702 " pdb=" C1 CO1 R 702 " pdb=" C5 CO1 R 702 " pdb=" C6 CO1 R 702 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.24e+00 ... (remaining 1430 not shown) Planarity restraints: 1609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA S 199 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.91e+00 pdb=" C ALA S 199 " -0.042 2.00e-02 2.50e+03 pdb=" O ALA S 199 " 0.016 2.00e-02 2.50e+03 pdb=" N PHE S 200 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 262 " -0.020 2.00e-02 2.50e+03 1.52e-02 4.61e+00 pdb=" CG TYR R 262 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR R 262 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR R 262 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR R 262 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR R 262 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR R 262 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR R 262 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 99 " 0.015 2.00e-02 2.50e+03 1.05e-02 2.75e+00 pdb=" CG TRP B 99 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP B 99 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP B 99 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 99 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 99 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 99 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 99 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 99 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 99 " 0.001 2.00e-02 2.50e+03 ... (remaining 1606 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 484 2.75 - 3.29: 9199 3.29 - 3.82: 14292 3.82 - 4.36: 18891 4.36 - 4.90: 31766 Nonbonded interactions: 74632 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.211 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.246 3.040 nonbonded pdb=" O SER S 196 " pdb=" O ALA S 199 " model vdw 2.279 3.040 nonbonded pdb=" OG1 THR R 349 " pdb=" O ARG A 32 " model vdw 2.325 3.040 nonbonded pdb=" O GLU R 292 " pdb=" NH2 ARG R 302 " model vdw 2.334 3.120 ... (remaining 74627 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.900 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 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 : 0.014 0.113 9425 Z= 1.040 Angle : 1.681 9.278 12787 Z= 1.246 Chirality : 0.083 0.455 1433 Planarity : 0.004 0.038 1609 Dihedral : 13.713 84.039 3338 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.10 % Allowed : 4.54 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.22), residues: 1152 helix: -0.79 (0.23), residues: 392 sheet: -2.30 (0.30), residues: 243 loop : -2.15 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 179 TYR 0.037 0.003 TYR R 262 PHE 0.020 0.003 PHE R 285 TRP 0.029 0.003 TRP B 99 HIS 0.008 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.01384 / 1.04 ( 9420) covalent geometry : angle 1.68168 / 1.25 (12777) SS BOND : bond 0.00596 / 0.31 ( 5) SS BOND : angle 1.34503 / 0.74 ( 10) hydrogen bonds : bond 0.15987 / 10.89 ( 446) hydrogen bonds : angle 7.24116 / 5.29 ( 1263) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 228 GLN cc_start: 0.8679 (mt0) cc_final: 0.8308 (mp10) REVERT: R 305 GLU cc_start: 0.6204 (tm-30) cc_final: 0.5867 (tm-30) REVERT: R 344 LYS cc_start: 0.8350 (tttt) cc_final: 0.7831 (ttpp) REVERT: R 519 LYS cc_start: 0.8079 (mttt) cc_final: 0.7796 (mtpp) REVERT: A 9 ASP cc_start: 0.7813 (m-30) cc_final: 0.7256 (m-30) REVERT: A 198 MET cc_start: 0.7863 (mtm) cc_final: 0.7524 (ttp) REVERT: B 6 GLN cc_start: 0.7619 (pp30) cc_final: 0.7182 (pp30) REVERT: B 29 THR cc_start: 0.8331 (m) cc_final: 0.7913 (p) REVERT: B 42 ARG cc_start: 0.8162 (ttp-110) cc_final: 0.7866 (ttp-110) REVERT: B 197 ARG cc_start: 0.8199 (mmm-85) cc_final: 0.7814 (tpp80) REVERT: G 18 GLN cc_start: 0.8099 (tp-100) cc_final: 0.7838 (tp40) REVERT: S 13 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8131 (tp40) REVERT: S 19 LYS cc_start: 0.8563 (ttpt) cc_final: 0.8298 (tttp) REVERT: S 76 LYS cc_start: 0.8768 (mmmm) cc_final: 0.8269 (mtmm) REVERT: S 89 GLU cc_start: 0.7724 (mp0) cc_final: 0.7496 (mp0) REVERT: S 174 GLN cc_start: 0.8494 (pt0) cc_final: 0.8144 (pt0) REVERT: S 210 GLU cc_start: 0.7849 (mp0) cc_final: 0.7489 (mp0) outliers start: 1 outliers final: 0 residues processed: 193 average time/residue: 0.1240 time to fit residues: 31.4930 Evaluate side-chains 145 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 202 ASN R 380 GLN R 396 ASN A 22 ASN A 195 HIS A 213 HIS A 306 GLN B 16 ASN B 266 HIS B 340 ASN S 167 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.130160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.096759 restraints weight = 13246.964| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.19 r_work: 0.3022 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9425 Z= 0.126 Angle : 0.567 7.795 12787 Z= 0.292 Chirality : 0.041 0.147 1433 Planarity : 0.004 0.050 1609 Dihedral : 5.419 85.764 1281 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.61 % Allowed : 10.80 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.24), residues: 1152 helix: 1.21 (0.26), residues: 401 sheet: -1.92 (0.28), residues: 276 loop : -1.65 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 291 TYR 0.018 0.001 TYR S 178 PHE 0.013 0.001 PHE A 189 TRP 0.009 0.001 TRP S 47 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 9420) covalent geometry : angle 0.56679 / 0.29 (12777) SS BOND : bond 0.00120 / 0.06 ( 5) SS BOND : angle 0.72229 / 0.42 ( 10) hydrogen bonds : bond 0.04113 / 2.77 ( 446) hydrogen bonds : angle 4.91072 / 3.60 ( 1263) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 228 GLN cc_start: 0.8731 (mt0) cc_final: 0.8400 (mp10) REVERT: R 230 MET cc_start: 0.8531 (mmm) cc_final: 0.7912 (tpp) REVERT: R 344 LYS cc_start: 0.8655 (tttt) cc_final: 0.8194 (ttpp) REVERT: A 52 GLN cc_start: 0.7623 (mt0) cc_final: 0.7385 (mt0) REVERT: B 8 ARG cc_start: 0.8237 (ttm170) cc_final: 0.7908 (mtp85) REVERT: B 101 MET cc_start: 0.9267 (mtp) cc_final: 0.9057 (mtp) REVERT: B 197 ARG cc_start: 0.8886 (mmm-85) cc_final: 0.8620 (tpp80) REVERT: G 47 GLU cc_start: 0.8711 (mp0) cc_final: 0.8440 (mt-10) REVERT: S 13 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8434 (tp40) REVERT: S 76 LYS cc_start: 0.8991 (mmmm) cc_final: 0.8677 (mtmm) REVERT: S 180 MET cc_start: 0.9011 (ptm) cc_final: 0.8635 (ptm) REVERT: S 210 GLU cc_start: 0.8176 (mp0) cc_final: 0.7903 (mp0) outliers start: 16 outliers final: 6 residues processed: 168 average time/residue: 0.1076 time to fit residues: 24.2665 Evaluate side-chains 152 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 146 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 160 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 105 optimal weight: 0.0670 chunk 106 optimal weight: 1.9990 chunk 21 optimal weight: 0.0870 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN B 91 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.132019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.099099 restraints weight = 13350.829| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.11 r_work: 0.3050 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9425 Z= 0.112 Angle : 0.533 8.926 12787 Z= 0.273 Chirality : 0.040 0.136 1433 Planarity : 0.003 0.052 1609 Dihedral : 5.216 88.612 1281 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.72 % Allowed : 13.52 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.25), residues: 1152 helix: 1.69 (0.27), residues: 403 sheet: -1.53 (0.28), residues: 276 loop : -1.51 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 52 TYR 0.017 0.001 TYR A 302 PHE 0.010 0.001 PHE A 189 TRP 0.011 0.001 TRP R 206 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 9420) covalent geometry : angle 0.53323 / 0.27 (12777) SS BOND : bond 0.00219 / 0.11 ( 5) SS BOND : angle 0.58250 / 0.38 ( 10) hydrogen bonds : bond 0.03588 / 2.42 ( 446) hydrogen bonds : angle 4.45499 / 3.26 ( 1263) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: R 228 GLN cc_start: 0.8659 (mt0) cc_final: 0.8349 (mp10) REVERT: R 230 MET cc_start: 0.8751 (mmm) cc_final: 0.8061 (tpp) REVERT: R 344 LYS cc_start: 0.8705 (tttt) cc_final: 0.8256 (ttpp) REVERT: R 515 LEU cc_start: 0.8609 (tp) cc_final: 0.8367 (tp) REVERT: A 276 GLU cc_start: 0.8220 (pp20) cc_final: 0.7973 (pp20) REVERT: B 8 ARG cc_start: 0.8266 (ttm170) cc_final: 0.7948 (mtp85) REVERT: B 197 ARG cc_start: 0.8892 (mmm-85) cc_final: 0.8588 (tpp80) REVERT: G 22 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8337 (tt0) REVERT: G 47 GLU cc_start: 0.8711 (mp0) cc_final: 0.8456 (mt-10) REVERT: S 13 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8477 (tp40) REVERT: S 210 GLU cc_start: 0.8237 (mp0) cc_final: 0.8003 (mp0) outliers start: 17 outliers final: 11 residues processed: 169 average time/residue: 0.1090 time to fit residues: 24.9819 Evaluate side-chains 159 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 1 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 396 ASN ** R 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.131559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.098630 restraints weight = 13398.114| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.11 r_work: 0.3045 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9425 Z= 0.122 Angle : 0.525 8.907 12787 Z= 0.267 Chirality : 0.040 0.136 1433 Planarity : 0.003 0.054 1609 Dihedral : 5.137 85.256 1281 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.12 % Allowed : 14.13 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.25), residues: 1152 helix: 1.79 (0.27), residues: 403 sheet: -1.34 (0.29), residues: 264 loop : -1.40 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 150 TYR 0.019 0.001 TYR A 302 PHE 0.011 0.001 PHE A 189 TRP 0.010 0.001 TRP R 206 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 9420) covalent geometry : angle 0.52512 / 0.27 (12777) SS BOND : bond 0.00152 / 0.08 ( 5) SS BOND : angle 0.59720 / 0.36 ( 10) hydrogen bonds : bond 0.03466 / 2.34 ( 446) hydrogen bonds : angle 4.29793 / 3.13 ( 1263) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: R 228 GLN cc_start: 0.8649 (mt0) cc_final: 0.8348 (mp10) REVERT: R 230 MET cc_start: 0.8816 (mmm) cc_final: 0.8267 (tpp) REVERT: R 344 LYS cc_start: 0.8702 (tttt) cc_final: 0.8261 (ttpp) REVERT: R 515 LEU cc_start: 0.8690 (tp) cc_final: 0.8431 (tp) REVERT: A 276 GLU cc_start: 0.8239 (pp20) cc_final: 0.7998 (pp20) REVERT: A 296 TYR cc_start: 0.8530 (t80) cc_final: 0.8314 (t80) REVERT: A 302 TYR cc_start: 0.9159 (t80) cc_final: 0.8782 (t80) REVERT: B 8 ARG cc_start: 0.8358 (ttm170) cc_final: 0.8062 (mtp85) REVERT: B 197 ARG cc_start: 0.8946 (mmm-85) cc_final: 0.8685 (tpp80) REVERT: G 47 GLU cc_start: 0.8690 (mp0) cc_final: 0.8486 (mt-10) REVERT: S 13 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8493 (tp40) REVERT: S 113 GLN cc_start: 0.8896 (tp40) cc_final: 0.8450 (mm-40) REVERT: S 210 GLU cc_start: 0.8256 (mp0) cc_final: 0.7996 (mp0) outliers start: 21 outliers final: 15 residues processed: 166 average time/residue: 0.1062 time to fit residues: 24.1452 Evaluate side-chains 164 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 47 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.122555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.089752 restraints weight = 13906.033| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.03 r_work: 0.2908 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 9425 Z= 0.243 Angle : 0.600 9.330 12787 Z= 0.305 Chirality : 0.043 0.166 1433 Planarity : 0.004 0.058 1609 Dihedral : 5.376 83.505 1281 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.03 % Allowed : 15.14 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.25), residues: 1152 helix: 1.67 (0.27), residues: 403 sheet: -1.54 (0.28), residues: 293 loop : -1.31 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 150 TYR 0.015 0.002 TYR A 302 PHE 0.015 0.001 PHE B 235 TRP 0.014 0.002 TRP S 47 HIS 0.004 0.001 HIS R 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.24 ( 9420) covalent geometry : angle 0.59976 / 0.31 (12777) SS BOND : bond 0.00163 / 0.08 ( 5) SS BOND : angle 0.79540 / 0.50 ( 10) hydrogen bonds : bond 0.03845 / 2.61 ( 446) hydrogen bonds : angle 4.44569 / 3.23 ( 1263) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 228 GLN cc_start: 0.8604 (mt0) cc_final: 0.8276 (mp10) REVERT: R 230 MET cc_start: 0.8861 (mmm) cc_final: 0.8350 (tpp) REVERT: R 344 LYS cc_start: 0.8835 (tttt) cc_final: 0.8468 (ttpp) REVERT: R 515 LEU cc_start: 0.8713 (tp) cc_final: 0.8448 (tp) REVERT: A 276 GLU cc_start: 0.8235 (pp20) cc_final: 0.7922 (tm-30) REVERT: A 296 TYR cc_start: 0.8591 (t80) cc_final: 0.8344 (t80) REVERT: A 302 TYR cc_start: 0.9318 (t80) cc_final: 0.8975 (t80) REVERT: B 8 ARG cc_start: 0.8374 (ttm170) cc_final: 0.8106 (mtp85) REVERT: B 234 PHE cc_start: 0.9504 (OUTLIER) cc_final: 0.9280 (m-80) REVERT: B 312 ASP cc_start: 0.8236 (m-30) cc_final: 0.8001 (t0) REVERT: G 47 GLU cc_start: 0.8691 (mp0) cc_final: 0.8481 (mt-10) REVERT: G 48 ASP cc_start: 0.8697 (t0) cc_final: 0.8463 (t0) REVERT: S 13 GLN cc_start: 0.8738 (mm-40) cc_final: 0.8526 (tp40) REVERT: S 113 GLN cc_start: 0.8977 (tp40) cc_final: 0.8544 (mm-40) REVERT: S 210 GLU cc_start: 0.8335 (mp0) cc_final: 0.8122 (mp0) outliers start: 30 outliers final: 23 residues processed: 168 average time/residue: 0.1049 time to fit residues: 24.0618 Evaluate side-chains 165 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 329 VAL Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 102 optimal weight: 0.9990 chunk 32 optimal weight: 0.0970 chunk 68 optimal weight: 0.0370 chunk 37 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.126929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.094958 restraints weight = 13780.587| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.98 r_work: 0.3007 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9425 Z= 0.109 Angle : 0.529 8.859 12787 Z= 0.269 Chirality : 0.040 0.133 1433 Planarity : 0.003 0.053 1609 Dihedral : 5.098 83.748 1281 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.02 % Allowed : 16.65 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.25), residues: 1152 helix: 1.91 (0.27), residues: 403 sheet: -1.36 (0.29), residues: 268 loop : -1.19 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 251 TYR 0.015 0.001 TYR S 178 PHE 0.010 0.001 PHE A 189 TRP 0.012 0.001 TRP R 206 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 9420) covalent geometry : angle 0.52911 / 0.27 (12777) SS BOND : bond 0.00192 / 0.10 ( 5) SS BOND : angle 0.49224 / 0.27 ( 10) hydrogen bonds : bond 0.03311 / 2.23 ( 446) hydrogen bonds : angle 4.20977 / 3.08 ( 1263) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: R 228 GLN cc_start: 0.8554 (mt0) cc_final: 0.8296 (mp10) REVERT: R 230 MET cc_start: 0.8882 (mmm) cc_final: 0.8356 (tpp) REVERT: R 344 LYS cc_start: 0.8684 (tttt) cc_final: 0.8286 (ttpp) REVERT: R 515 LEU cc_start: 0.8718 (tp) cc_final: 0.8464 (tp) REVERT: A 186 GLU cc_start: 0.8227 (tt0) cc_final: 0.8023 (tt0) REVERT: A 187 THR cc_start: 0.8982 (OUTLIER) cc_final: 0.8782 (p) REVERT: A 276 GLU cc_start: 0.8238 (pp20) cc_final: 0.7958 (tm-30) REVERT: A 296 TYR cc_start: 0.8581 (t80) cc_final: 0.8346 (t80) REVERT: A 302 TYR cc_start: 0.9251 (t80) cc_final: 0.8867 (t80) REVERT: B 8 ARG cc_start: 0.8355 (ttm170) cc_final: 0.8097 (mtp85) REVERT: G 22 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8309 (tt0) REVERT: G 47 GLU cc_start: 0.8618 (mp0) cc_final: 0.8418 (mt-10) REVERT: S 113 GLN cc_start: 0.8912 (tp40) cc_final: 0.8513 (mm-40) REVERT: S 180 MET cc_start: 0.8896 (ptm) cc_final: 0.8605 (ptm) REVERT: S 208 GLU cc_start: 0.8589 (pt0) cc_final: 0.7751 (pt0) REVERT: S 210 GLU cc_start: 0.8197 (mp0) cc_final: 0.7782 (mp0) outliers start: 20 outliers final: 15 residues processed: 168 average time/residue: 0.1030 time to fit residues: 23.9256 Evaluate side-chains 159 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 311 THR Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 50 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 0.0570 chunk 82 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 12 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 ASN A 306 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.129644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.097304 restraints weight = 13642.663| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.00 r_work: 0.3036 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9425 Z= 0.113 Angle : 0.519 8.940 12787 Z= 0.265 Chirality : 0.040 0.131 1433 Planarity : 0.003 0.056 1609 Dihedral : 5.051 83.142 1281 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.12 % Allowed : 17.46 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.25), residues: 1152 helix: 1.97 (0.27), residues: 403 sheet: -1.30 (0.29), residues: 277 loop : -1.08 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 150 TYR 0.015 0.001 TYR A 302 PHE 0.009 0.001 PHE A 189 TRP 0.012 0.001 TRP R 206 HIS 0.003 0.001 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 9420) covalent geometry : angle 0.51921 / 0.26 (12777) SS BOND : bond 0.00141 / 0.07 ( 5) SS BOND : angle 0.63012 / 0.38 ( 10) hydrogen bonds : bond 0.03278 / 2.21 ( 446) hydrogen bonds : angle 4.09766 / 2.98 ( 1263) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: R 228 GLN cc_start: 0.8586 (mt0) cc_final: 0.8301 (mp10) REVERT: R 230 MET cc_start: 0.8877 (mmm) cc_final: 0.8391 (tpp) REVERT: R 344 LYS cc_start: 0.8690 (tttt) cc_final: 0.8284 (ttpp) REVERT: R 515 LEU cc_start: 0.8746 (tp) cc_final: 0.8509 (tp) REVERT: A 187 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8734 (p) REVERT: A 276 GLU cc_start: 0.8232 (pp20) cc_final: 0.7958 (tm-30) REVERT: A 296 TYR cc_start: 0.8539 (t80) cc_final: 0.8270 (t80) REVERT: A 302 TYR cc_start: 0.9202 (t80) cc_final: 0.8820 (t80) REVERT: B 8 ARG cc_start: 0.8362 (ttm170) cc_final: 0.8053 (mtp85) REVERT: G 22 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8340 (tt0) REVERT: S 113 GLN cc_start: 0.8836 (tp40) cc_final: 0.8426 (mm-40) REVERT: S 180 MET cc_start: 0.8898 (ptm) cc_final: 0.8592 (ptm) REVERT: S 208 GLU cc_start: 0.8483 (pt0) cc_final: 0.7623 (pt0) REVERT: S 210 GLU cc_start: 0.8223 (mp0) cc_final: 0.7746 (mp0) outliers start: 21 outliers final: 17 residues processed: 165 average time/residue: 0.1098 time to fit residues: 24.6991 Evaluate side-chains 162 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 311 THR Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 90 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 108 optimal weight: 0.1980 chunk 96 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 ASN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.126796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.094429 restraints weight = 13561.563| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.97 r_work: 0.2987 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9425 Z= 0.181 Angle : 0.574 9.255 12787 Z= 0.291 Chirality : 0.041 0.149 1433 Planarity : 0.004 0.056 1609 Dihedral : 5.177 81.686 1281 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.72 % Allowed : 17.56 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.25), residues: 1152 helix: 1.87 (0.27), residues: 404 sheet: -1.23 (0.28), residues: 296 loop : -1.08 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.017 0.002 TYR A 302 PHE 0.011 0.001 PHE B 235 TRP 0.010 0.001 TRP S 47 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 ( 9420) covalent geometry : angle 0.57406 / 0.29 (12777) SS BOND : bond 0.00142 / 0.07 ( 5) SS BOND : angle 0.72575 / 0.45 ( 10) hydrogen bonds : bond 0.03513 / 2.37 ( 446) hydrogen bonds : angle 4.19834 / 3.04 ( 1263) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: R 228 GLN cc_start: 0.8577 (mt0) cc_final: 0.8270 (mp10) REVERT: R 230 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8416 (tpp) REVERT: R 344 LYS cc_start: 0.8769 (tttt) cc_final: 0.8396 (ttpp) REVERT: R 515 LEU cc_start: 0.8761 (tp) cc_final: 0.8512 (tp) REVERT: A 276 GLU cc_start: 0.8180 (pp20) cc_final: 0.7907 (tm-30) REVERT: A 302 TYR cc_start: 0.9175 (t80) cc_final: 0.8798 (t80) REVERT: B 8 ARG cc_start: 0.8364 (ttm170) cc_final: 0.8097 (mtp85) REVERT: B 58 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.9023 (pt) REVERT: G 22 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8276 (tt0) REVERT: S 113 GLN cc_start: 0.8883 (tp40) cc_final: 0.8471 (mm-40) REVERT: S 210 GLU cc_start: 0.8229 (mp0) cc_final: 0.8002 (mp0) outliers start: 27 outliers final: 20 residues processed: 165 average time/residue: 0.1101 time to fit residues: 25.0008 Evaluate side-chains 168 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 230 MET Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 311 THR Chi-restraints excluded: chain R residue 329 VAL Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 39 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 2 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 433 HIS A 22 ASN A 306 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.128960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.096876 restraints weight = 13608.952| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.96 r_work: 0.3031 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9425 Z= 0.121 Angle : 0.547 10.138 12787 Z= 0.276 Chirality : 0.040 0.133 1433 Planarity : 0.003 0.055 1609 Dihedral : 5.093 81.883 1281 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.12 % Allowed : 17.86 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.25), residues: 1152 helix: 1.94 (0.27), residues: 404 sheet: -1.16 (0.30), residues: 277 loop : -1.03 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 150 TYR 0.018 0.001 TYR A 302 PHE 0.011 0.001 PHE B 234 TRP 0.012 0.001 TRP R 206 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 9420) covalent geometry : angle 0.54679 / 0.28 (12777) SS BOND : bond 0.00123 / 0.06 ( 5) SS BOND : angle 0.59299 / 0.35 ( 10) hydrogen bonds : bond 0.03312 / 2.23 ( 446) hydrogen bonds : angle 4.10527 / 2.99 ( 1263) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: R 228 GLN cc_start: 0.8608 (mt0) cc_final: 0.8303 (mp10) REVERT: R 230 MET cc_start: 0.8872 (mmm) cc_final: 0.8417 (tpp) REVERT: R 344 LYS cc_start: 0.8693 (tttt) cc_final: 0.8281 (ttpp) REVERT: R 515 LEU cc_start: 0.8743 (tp) cc_final: 0.8499 (tp) REVERT: A 187 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8743 (p) REVERT: A 276 GLU cc_start: 0.8191 (pp20) cc_final: 0.7900 (tm-30) REVERT: A 302 TYR cc_start: 0.9122 (t80) cc_final: 0.8792 (t80) REVERT: B 8 ARG cc_start: 0.8368 (ttm170) cc_final: 0.8095 (mtp85) REVERT: B 58 ILE cc_start: 0.9254 (OUTLIER) cc_final: 0.8961 (pt) REVERT: B 172 GLU cc_start: 0.7818 (pm20) cc_final: 0.7586 (pm20) REVERT: G 22 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8306 (tt0) REVERT: S 113 GLN cc_start: 0.8874 (tp40) cc_final: 0.8453 (mm-40) REVERT: S 180 MET cc_start: 0.8912 (ptm) cc_final: 0.8582 (ptm) REVERT: S 210 GLU cc_start: 0.8255 (mp0) cc_final: 0.7884 (mp0) outliers start: 21 outliers final: 18 residues processed: 162 average time/residue: 0.1067 time to fit residues: 23.8328 Evaluate side-chains 164 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 311 THR Chi-restraints excluded: chain R residue 329 VAL Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 41 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 44 optimal weight: 0.2980 chunk 49 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 98 optimal weight: 0.2980 chunk 74 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 47 optimal weight: 0.0570 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 ASN A 304 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.129448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.097079 restraints weight = 13616.990| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.99 r_work: 0.3028 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9425 Z= 0.130 Angle : 0.555 10.350 12787 Z= 0.281 Chirality : 0.040 0.136 1433 Planarity : 0.003 0.056 1609 Dihedral : 5.066 80.867 1281 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.52 % Allowed : 17.86 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.25), residues: 1152 helix: 1.92 (0.27), residues: 405 sheet: -1.06 (0.30), residues: 277 loop : -1.01 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 214 TYR 0.018 0.001 TYR A 302 PHE 0.012 0.001 PHE B 234 TRP 0.012 0.001 TRP R 206 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 9420) covalent geometry : angle 0.55465 / 0.28 (12777) SS BOND : bond 0.00127 / 0.07 ( 5) SS BOND : angle 0.60843 / 0.37 ( 10) hydrogen bonds : bond 0.03323 / 2.24 ( 446) hydrogen bonds : angle 4.08602 / 2.97 ( 1263) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 228 GLN cc_start: 0.8589 (mt0) cc_final: 0.8293 (mp10) REVERT: R 230 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8441 (tpp) REVERT: R 344 LYS cc_start: 0.8721 (tttt) cc_final: 0.8315 (ttpp) REVERT: R 515 LEU cc_start: 0.8762 (tp) cc_final: 0.8520 (tp) REVERT: A 187 THR cc_start: 0.8976 (OUTLIER) cc_final: 0.8748 (p) REVERT: A 276 GLU cc_start: 0.8174 (pp20) cc_final: 0.7936 (pp20) REVERT: A 302 TYR cc_start: 0.9043 (t80) cc_final: 0.8753 (t80) REVERT: B 8 ARG cc_start: 0.8355 (ttm170) cc_final: 0.8078 (mtp85) REVERT: B 58 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.9019 (pt) REVERT: G 22 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8165 (tt0) REVERT: S 113 GLN cc_start: 0.8888 (tp40) cc_final: 0.8465 (mm-40) REVERT: S 180 MET cc_start: 0.8900 (ptm) cc_final: 0.8573 (ptm) REVERT: S 210 GLU cc_start: 0.8231 (mp0) cc_final: 0.7930 (mp0) outliers start: 25 outliers final: 20 residues processed: 162 average time/residue: 0.1023 time to fit residues: 23.0340 Evaluate side-chains 162 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 230 MET Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 311 THR Chi-restraints excluded: chain R residue 329 VAL Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 234 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 84 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 45 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 56 optimal weight: 0.0170 chunk 78 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 ASN A 304 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.130449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.099142 restraints weight = 13356.562| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.04 r_work: 0.3061 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9425 Z= 0.113 Angle : 0.555 10.823 12787 Z= 0.282 Chirality : 0.040 0.142 1433 Planarity : 0.003 0.056 1609 Dihedral : 5.022 81.392 1281 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.32 % Allowed : 18.26 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.25), residues: 1152 helix: 1.95 (0.27), residues: 404 sheet: -0.87 (0.30), residues: 267 loop : -1.04 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 400 TYR 0.020 0.001 TYR A 302 PHE 0.011 0.001 PHE B 234 TRP 0.017 0.001 TRP R 537 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 9420) covalent geometry : angle 0.55443 / 0.28 (12777) SS BOND : bond 0.00136 / 0.07 ( 5) SS BOND : angle 0.65033 / 0.47 ( 10) hydrogen bonds : bond 0.03226 / 2.16 ( 446) hydrogen bonds : angle 4.03509 / 2.94 ( 1263) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2786.06 seconds wall clock time: 48 minutes 28.55 seconds (2908.55 seconds total)