Starting phenix.real_space_refine on Sat Jul 4 04:38:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5g2x_3331/07_2026/5g2x_3331.cif Found real_map, /net/cci-nas-00/data/ceres_data/5g2x_3331/07_2026/5g2x_3331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5g2x_3331/07_2026/5g2x_3331.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5g2x_3331/07_2026/5g2x_3331.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5g2x_3331/07_2026/5g2x_3331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5g2x_3331/07_2026/5g2x_3331.map" restraint_files = "/net/cci-nas-00/data/ceres_data/5g2x_3331/07_2026/5g2x_3331.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5g2x_3331/07_2026/5g2x_3331.cif" } resolution = 3.8 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= 0.001 sd= 0.006 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: 5 Type Number sf(0) Gaussians P 703 5.49 5 S 19 5.16 5 C 9320 2.51 5 N 3467 2.21 5 O 5563 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19072 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 14825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 14825 Classifications: {'RNA': 692} Modifications used: {'5*END': 1, 'rna2p_pur': 64, 'rna2p_pyr': 34, 'rna3p_pur': 345, 'rna3p_pyr': 249} Link IDs: {'rna2p': 97, 'rna3p': 594} Chain breaks: 3 Chain: "B" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 250 Classifications: {'RNA': 12} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 10} Chain: "C" Number of atoms: 3997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3997 Classifications: {'peptide': 487} Link IDs: {'CIS': 24, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 447} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 4.13, per 1000 atoms: 0.22 Number of scatterers: 19072 At special positions: 0 Unit cell: (156.785, 152.865, 139.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 P 703 15.00 O 5563 8.00 N 3467 7.00 C 9320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.79 Conformation dependent library (CDL) restraints added in 369.7 milliseconds 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 918 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 0 sheets defined 36.6% alpha, 0.0% beta 42 base pairs and 325 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain 'C' and resid 5 through 13 removed outlier: 4.153A pdb=" N GLU C 9 " --> pdb=" O MET C 5 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG C 10 " --> pdb=" O ALA C 6 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE C 11 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER C 12 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS C 13 " --> pdb=" O GLU C 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 5 through 13' Processing helix chain 'C' and resid 30 through 41 removed outlier: 4.746A pdb=" N ASP C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ILE C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TYR C 36 " --> pdb=" O ARG C 32 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL C 38 " --> pdb=" O ASP C 34 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR C 40 " --> pdb=" O TYR C 36 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLN C 41 " --> pdb=" O TYR C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 73 removed outlier: 3.559A pdb=" N GLN C 72 " --> pdb=" O LYS C 68 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 68 through 73' Processing helix chain 'C' and resid 106 through 121 removed outlier: 3.807A pdb=" N ILE C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN C 111 " --> pdb=" O ASP C 107 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLU C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ALA C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ILE C 116 " --> pdb=" O GLU C 112 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C 121 " --> pdb=" O ILE C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 148 removed outlier: 4.273A pdb=" N LYS C 144 " --> pdb=" O HIS C 140 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR C 145 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE C 146 " --> pdb=" O ALA C 142 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LYS C 147 " --> pdb=" O LEU C 143 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG C 148 " --> pdb=" O LYS C 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 140 through 148' Processing helix chain 'C' and resid 171 through 179 removed outlier: 4.416A pdb=" N ILE C 177 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN C 178 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LEU C 179 " --> pdb=" O GLY C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 197 removed outlier: 7.577A pdb=" N TYR C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LYS C 192 " --> pdb=" O GLN C 188 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU C 194 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LYS C 195 " --> pdb=" O TYR C 191 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ALA C 196 " --> pdb=" O LYS C 192 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N GLY C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 187 through 197' Processing helix chain 'C' and resid 217 through 248 removed outlier: 3.815A pdb=" N ASN C 223 " --> pdb=" O PRO C 219 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 226 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU C 229 " --> pdb=" O TYR C 225 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS C 231 " --> pdb=" O HIS C 227 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN C 235 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LEU C 236 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS C 237 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS C 239 " --> pdb=" O GLN C 235 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP C 241 " --> pdb=" O LYS C 237 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ARG C 242 " --> pdb=" O MET C 238 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU C 243 " --> pdb=" O LYS C 239 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N SER C 244 " --> pdb=" O PHE C 240 " (cutoff:3.500A) Proline residue: C 245 - end of helix removed outlier: 4.466A pdb=" N ILE C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 331 removed outlier: 3.874A pdb=" N GLN C 322 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TRP C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ILE C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS C 325 " --> pdb=" O CYS C 321 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU C 326 " --> pdb=" O GLN C 322 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 328 " --> pdb=" O ILE C 324 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS C 329 " --> pdb=" O LYS C 325 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 331 " --> pdb=" O GLN C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 343 No H-bonds generated for 'chain 'C' and resid 341 through 343' Processing helix chain 'C' and resid 393 through 400 removed outlier: 4.603A pdb=" N PHE C 397 " --> pdb=" O LYS C 393 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ILE C 398 " --> pdb=" O ILE C 394 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N PHE C 399 " --> pdb=" O ARG C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 440 removed outlier: 3.952A pdb=" N ILE C 429 " --> pdb=" O ASP C 425 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE C 431 " --> pdb=" O GLU C 427 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR C 432 " --> pdb=" O ILE C 428 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG C 437 " --> pdb=" O ASN C 433 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLY C 438 " --> pdb=" O SER C 434 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE C 439 " --> pdb=" O GLU C 435 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N CYS C 440 " --> pdb=" O LEU C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 470 removed outlier: 3.550A pdb=" N ALA C 456 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR C 457 " --> pdb=" O ASN C 453 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU C 458 " --> pdb=" O TYR C 454 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N MET C 459 " --> pdb=" O PHE C 455 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR C 461 " --> pdb=" O TYR C 457 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER C 462 " --> pdb=" O LEU C 458 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS C 463 " --> pdb=" O MET C 459 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU C 464 " --> pdb=" O GLU C 460 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR C 466 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE C 467 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS C 470 " --> pdb=" O THR C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 538 removed outlier: 4.339A pdb=" N THR C 533 " --> pdb=" O TYR C 529 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU C 535 " --> pdb=" O ARG C 531 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG C 537 " --> pdb=" O THR C 533 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU C 538 " --> pdb=" O LEU C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 553 No H-bonds generated for 'chain 'C' and resid 552 through 553' 31 hydrogen bonds defined for protein. 93 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 325 stacking parallelities Total time for adding SS restraints: 4.00 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3171 1.34 - 1.45: 9106 1.45 - 1.57: 7265 1.57 - 1.69: 1402 1.69 - 1.81: 28 Bond restraints: 20972 Sorted by residual: bond pdb=" C HIS C 591 " pdb=" N ARG C 592 " ideal model delta sigma weight residual 1.329 1.231 0.098 1.40e-02 5.10e+03 4.87e+01 bond pdb=" CA ASN C 18 " pdb=" C ASN C 18 " ideal model delta sigma weight residual 1.523 1.554 -0.031 1.34e-02 5.57e+03 5.28e+00 bond pdb=" CA TYR C 527 " pdb=" C TYR C 527 " ideal model delta sigma weight residual 1.520 1.551 -0.032 1.40e-02 5.10e+03 5.15e+00 bond pdb=" CA TYR C 44 " pdb=" C TYR C 44 " ideal model delta sigma weight residual 1.524 1.547 -0.024 1.26e-02 6.30e+03 3.53e+00 bond pdb=" CA ASN C 46 " pdb=" C ASN C 46 " ideal model delta sigma weight residual 1.524 1.546 -0.023 1.26e-02 6.30e+03 3.23e+00 ... (remaining 20967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 31660 2.20 - 4.40: 120 4.40 - 6.60: 20 6.60 - 8.79: 3 8.79 - 10.99: 1 Bond angle restraints: 31804 Sorted by residual: angle pdb=" C ASN C 18 " pdb=" N ILE C 19 " pdb=" CA ILE C 19 " ideal model delta sigma weight residual 121.70 132.69 -10.99 1.80e+00 3.09e-01 3.73e+01 angle pdb=" CA ASN C 18 " pdb=" C ASN C 18 " pdb=" N ILE C 19 " ideal model delta sigma weight residual 116.84 124.40 -7.56 1.71e+00 3.42e-01 1.95e+01 angle pdb=" C VAL C 375 " pdb=" N LYS C 376 " pdb=" CA LYS C 376 " ideal model delta sigma weight residual 121.70 129.32 -7.62 1.80e+00 3.09e-01 1.79e+01 angle pdb=" C LEU C 100 " pdb=" CA LEU C 100 " pdb=" CB LEU C 100 " ideal model delta sigma weight residual 116.54 110.38 6.16 1.46e+00 4.69e-01 1.78e+01 angle pdb=" CA GLY C 48 " pdb=" C GLY C 48 " pdb=" O GLY C 48 " ideal model delta sigma weight residual 122.76 118.42 4.34 1.12e+00 7.97e-01 1.50e+01 ... (remaining 31799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 10688 35.59 - 71.19: 188 71.19 - 106.78: 22 106.78 - 142.37: 3 142.37 - 177.96: 8 Dihedral angle restraints: 10909 sinusoidal: 9481 harmonic: 1428 Sorted by residual: dihedral pdb=" O4' C A 316 " pdb=" C1' C A 316 " pdb=" N1 C A 316 " pdb=" C2 C A 316 " ideal model delta sinusoidal sigma weight residual -128.00 49.96 -177.96 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C A 487 " pdb=" C1' C A 487 " pdb=" N1 C A 487 " pdb=" C2 C A 487 " ideal model delta sinusoidal sigma weight residual -128.00 48.87 -176.87 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" C4' U A 177 " pdb=" C3' U A 177 " pdb=" O3' U A 177 " pdb=" P A A 178 " ideal model delta sinusoidal sigma weight residual -110.00 63.48 -173.48 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 10906 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3898 0.036 - 0.073: 155 0.073 - 0.109: 43 0.109 - 0.146: 10 0.146 - 0.182: 8 Chirality restraints: 4114 Sorted by residual: chirality pdb=" C3' A A 149 " pdb=" C4' A A 149 " pdb=" O3' A A 149 " pdb=" C2' A A 149 " both_signs ideal model delta sigma weight residual False -2.74 -2.56 -0.18 2.00e-01 2.50e+01 8.30e-01 chirality pdb=" C3' C B 1 " pdb=" C4' C B 1 " pdb=" O3' C B 1 " pdb=" C2' C B 1 " both_signs ideal model delta sigma weight residual False -2.48 -2.66 0.18 2.00e-01 2.50e+01 7.99e-01 chirality pdb=" C3' G A 559 " pdb=" C4' G A 559 " pdb=" O3' G A 559 " pdb=" C2' G A 559 " both_signs ideal model delta sigma weight residual False -2.74 -2.57 -0.18 2.00e-01 2.50e+01 7.83e-01 ... (remaining 4111 not shown) Planarity restraints: 1389 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 123 " 0.030 5.00e-02 4.00e+02 4.58e-02 3.35e+00 pdb=" N PRO C 124 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 124 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 124 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 218 " -0.014 5.00e-02 4.00e+02 2.12e-02 7.21e-01 pdb=" N PRO C 219 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO C 219 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO C 219 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 211 " -0.013 5.00e-02 4.00e+02 1.96e-02 6.16e-01 pdb=" N PRO C 212 " 0.034 5.00e-02 4.00e+02 pdb=" CA PRO C 212 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO C 212 " -0.011 5.00e-02 4.00e+02 ... (remaining 1386 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2529 2.76 - 3.29: 15686 3.29 - 3.83: 33394 3.83 - 4.36: 40872 4.36 - 4.90: 54857 Nonbonded interactions: 147338 Sorted by model distance: nonbonded pdb=" O2' C B 1 " pdb=" O4' A B 2 " model vdw 2.219 3.040 nonbonded pdb=" O2' C A2395 " pdb=" O5' A A2396 " model vdw 2.278 3.040 nonbonded pdb=" O2' C A 7 " pdb=" O2' A A 516 " model vdw 2.289 3.040 nonbonded pdb=" O ARG C 25 " pdb=" OH TYR C 29 " model vdw 2.290 3.040 nonbonded pdb=" OP2 A A 563 " pdb=" OH TYR C 36 " model vdw 2.295 3.040 ... (remaining 147333 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 group one per residue 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: 0.820 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.150 Find NCS groups from input model: 0.060 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2984 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 : 0.001 0.098 20972 Z= 0.090 Angle : 0.321 10.992 31804 Z= 0.186 Chirality : 0.018 0.182 4114 Planarity : 0.002 0.046 1389 Dihedral : 11.564 177.965 9991 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 5.88 % Allowed : 19.75 % Favored : 74.37 % Rotamer: Outliers : 0.45 % Allowed : 1.59 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 5.15 % Twisted Proline : 0.00 % 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: -5.72 (0.28), residues: 476 helix: -4.59 (0.17), residues: 102 sheet: -4.08 (1.23), residues: 9 loop : -3.91 (0.26), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 154 TYR 0.007 0.000 TYR C 204 PHE 0.003 0.000 PHE C 156 TRP 0.003 0.000 TRP C 202 HIS 0.001 0.000 HIS C 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00137 / 0.09 (20972) covalent geometry : angle 0.32118 / 0.19 (31804) hydrogen bonds : bond 0.32553 / 19.38 ( 120) hydrogen bonds : angle 12.98927 / 8.25 ( 247) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 123 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 481 MET cc_start: 0.5012 (mmt) cc_final: 0.4804 (mmm) outliers start: 2 outliers final: 1 residues processed: 124 average time/residue: 0.1580 time to fit residues: 28.3839 Evaluate side-chains 65 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 390 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 40.0000 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 82 GLN ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 GLN C 223 ASN C 381 ASN ** C 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.127831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.109874 restraints weight = 115221.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.110515 restraints weight = 64849.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.111166 restraints weight = 47691.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.111408 restraints weight = 35720.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.111382 restraints weight = 33708.403| |-----------------------------------------------------------------------------| r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6207 moved from start: 0.6408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 20972 Z= 0.394 Angle : 1.154 13.408 31804 Z= 0.560 Chirality : 0.051 0.297 4114 Planarity : 0.008 0.076 1389 Dihedral : 15.978 178.915 8971 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 28.64 Ramachandran Plot: Outliers : 1.26 % Allowed : 17.44 % Favored : 81.30 % Rotamer: Outliers : 4.31 % Allowed : 11.11 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 5.15 % Twisted Proline : 0.00 % 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: -5.12 (0.31), residues: 476 helix: -3.07 (0.33), residues: 126 sheet: None (None), residues: 0 loop : -3.87 (0.28), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG C 115 TYR 0.032 0.005 TYR C 303 PHE 0.031 0.004 PHE C 310 TRP 0.019 0.003 TRP C 412 HIS 0.012 0.003 HIS C 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00746 / 0.39 (20972) covalent geometry : angle 1.15368 / 0.56 (31804) hydrogen bonds : bond 0.17328 / 10.70 ( 120) hydrogen bonds : angle 5.15816 / 2.94 ( 247) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 155 TRP cc_start: 0.3729 (m-10) cc_final: 0.3469 (m-10) REVERT: C 305 ARG cc_start: 0.6186 (ptt90) cc_final: 0.5395 (ptt90) REVERT: C 342 GLU cc_start: 0.5954 (pm20) cc_final: 0.5571 (pm20) REVERT: C 479 ILE cc_start: 0.7230 (mt) cc_final: 0.6971 (mm) REVERT: C 499 LYS cc_start: 0.3366 (OUTLIER) cc_final: 0.1487 (tttt) REVERT: C 500 GLN cc_start: 0.3823 (OUTLIER) cc_final: 0.3542 (tt0) outliers start: 19 outliers final: 6 residues processed: 94 average time/residue: 0.1521 time to fit residues: 21.8341 Evaluate side-chains 63 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 167 ASN Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain C residue 499 LYS Chi-restraints excluded: chain C residue 500 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 102 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 88 optimal weight: 0.0670 chunk 18 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 62 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 overall best weight: 0.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 167 ASN ** C 433 ASN ** 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 = 0.4645 r_free = 0.4645 target = 0.132352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.116117 restraints weight = 115700.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.117480 restraints weight = 60739.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.117707 restraints weight = 48484.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.118223 restraints weight = 48144.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.118106 restraints weight = 36972.577| |-----------------------------------------------------------------------------| r_work (final): 0.4337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5892 moved from start: 0.6073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20972 Z= 0.122 Angle : 0.591 12.852 31804 Z= 0.299 Chirality : 0.030 0.191 4114 Planarity : 0.004 0.046 1389 Dihedral : 15.236 178.113 8969 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 1.05 % Allowed : 17.02 % Favored : 81.93 % Rotamer: Outliers : 2.95 % Allowed : 16.33 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 5.15 % Twisted Proline : 0.00 % 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: -4.40 (0.33), residues: 476 helix: -1.76 (0.47), residues: 106 sheet: -3.17 (1.35), residues: 12 loop : -3.62 (0.28), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 437 TYR 0.012 0.001 TYR C 306 PHE 0.014 0.001 PHE C 310 TRP 0.006 0.001 TRP C 412 HIS 0.007 0.001 HIS C 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.12 (20972) covalent geometry : angle 0.59127 / 0.30 (31804) hydrogen bonds : bond 0.09689 / 5.95 ( 120) hydrogen bonds : angle 3.87529 / 2.25 ( 247) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 97 MET cc_start: 0.3657 (mmp) cc_final: 0.3382 (mmm) REVERT: C 155 TRP cc_start: 0.3416 (m-10) cc_final: 0.3089 (m-10) REVERT: C 305 ARG cc_start: 0.6136 (ptt90) cc_final: 0.5461 (ptt90) REVERT: C 342 GLU cc_start: 0.6115 (pm20) cc_final: 0.5764 (pm20) REVERT: C 386 LEU cc_start: 0.4520 (OUTLIER) cc_final: 0.4213 (pp) REVERT: C 452 LEU cc_start: 0.7375 (tp) cc_final: 0.7126 (tp) REVERT: C 481 MET cc_start: 0.5962 (mmt) cc_final: 0.5253 (mmm) outliers start: 13 outliers final: 8 residues processed: 71 average time/residue: 0.1298 time to fit residues: 14.6402 Evaluate side-chains 57 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 167 ASN Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 424 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 39 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 75 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 67 optimal weight: 40.0000 chunk 111 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 overall best weight: 6.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 93 ASN ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 ASN ** C 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 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 = 0.4451 r_free = 0.4451 target = 0.116938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.096659 restraints weight = 104502.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.097267 restraints weight = 52493.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.097618 restraints weight = 46376.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.097840 restraints weight = 39947.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.097956 restraints weight = 35780.377| |-----------------------------------------------------------------------------| r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.9175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 20972 Z= 0.373 Angle : 1.070 13.134 31804 Z= 0.530 Chirality : 0.052 0.291 4114 Planarity : 0.007 0.067 1389 Dihedral : 17.983 173.132 8969 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 32.87 Ramachandran Plot: Outliers : 1.26 % Allowed : 19.96 % Favored : 78.78 % Rotamer: Outliers : 5.44 % Allowed : 17.91 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 5.15 % Twisted Proline : 0.00 % 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: -5.08 (0.30), residues: 476 helix: -2.50 (0.38), residues: 126 sheet: None (None), residues: 0 loop : -4.09 (0.26), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 355 TYR 0.040 0.004 TYR C 225 PHE 0.021 0.003 PHE C 62 TRP 0.018 0.003 TRP C 412 HIS 0.012 0.003 HIS C 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00697 / 0.37 (20972) covalent geometry : angle 1.06973 / 0.53 (31804) hydrogen bonds : bond 0.16901 / 10.26 ( 120) hydrogen bonds : angle 5.16054 / 2.97 ( 247) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 386 LEU cc_start: 0.5054 (OUTLIER) cc_final: 0.4643 (pp) REVERT: C 424 THR cc_start: 0.7508 (OUTLIER) cc_final: 0.7308 (p) outliers start: 24 outliers final: 12 residues processed: 85 average time/residue: 0.1317 time to fit residues: 17.6739 Evaluate side-chains 68 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 424 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 109 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 8 optimal weight: 20.0000 chunk 41 optimal weight: 50.0000 chunk 50 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 ASN ** C 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 ASN ** C 451 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 = 0.4442 r_free = 0.4442 target = 0.116065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.094367 restraints weight = 107385.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.096979 restraints weight = 52269.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.096918 restraints weight = 32906.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.096967 restraints weight = 28381.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.097271 restraints weight = 28123.363| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 1.0370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 20972 Z= 0.313 Angle : 0.895 13.254 31804 Z= 0.450 Chirality : 0.045 0.282 4114 Planarity : 0.006 0.070 1389 Dihedral : 18.755 174.458 8969 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 28.84 Ramachandran Plot: Outliers : 0.84 % Allowed : 18.91 % Favored : 80.25 % Rotamer: Outliers : 5.67 % Allowed : 20.63 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 5.15 % Twisted Proline : 0.00 % 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: -5.37 (0.29), residues: 476 helix: -2.86 (0.35), residues: 142 sheet: -4.43 (1.18), residues: 10 loop : -4.20 (0.26), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 437 TYR 0.027 0.003 TYR C 442 PHE 0.021 0.003 PHE C 331 TRP 0.013 0.003 TRP C 489 HIS 0.011 0.003 HIS C 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.31 (20972) covalent geometry : angle 0.89458 / 0.45 (31804) hydrogen bonds : bond 0.13951 / 8.41 ( 120) hydrogen bonds : angle 4.97513 / 2.78 ( 247) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 111 GLN cc_start: 0.7876 (tp40) cc_final: 0.7644 (tp-100) REVERT: C 386 LEU cc_start: 0.4938 (OUTLIER) cc_final: 0.4539 (pp) REVERT: C 426 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.6895 (mm) REVERT: C 481 MET cc_start: 0.5956 (mmt) cc_final: 0.5521 (mmm) REVERT: C 494 GLU cc_start: 0.1939 (OUTLIER) cc_final: 0.0764 (pm20) outliers start: 25 outliers final: 12 residues processed: 83 average time/residue: 0.1403 time to fit residues: 18.0955 Evaluate side-chains 71 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 167 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 494 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 43 optimal weight: 40.0000 chunk 72 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.116011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.094057 restraints weight = 102379.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.097152 restraints weight = 47687.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.096776 restraints weight = 32222.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.096845 restraints weight = 26132.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.096837 restraints weight = 23786.395| |-----------------------------------------------------------------------------| r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 1.0846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20972 Z= 0.255 Angle : 0.820 13.019 31804 Z= 0.414 Chirality : 0.041 0.258 4114 Planarity : 0.006 0.057 1389 Dihedral : 18.767 177.184 8969 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 27.37 Ramachandran Plot: Outliers : 0.84 % Allowed : 19.75 % Favored : 79.41 % Rotamer: Outliers : 6.35 % Allowed : 21.77 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 5.15 % Twisted Proline : 0.00 % 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: -5.04 (0.31), residues: 476 helix: -2.53 (0.36), residues: 140 sheet: -4.34 (1.13), residues: 10 loop : -4.01 (0.28), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 115 TYR 0.021 0.003 TYR C 36 PHE 0.023 0.003 PHE C 23 TRP 0.008 0.002 TRP C 323 HIS 0.009 0.002 HIS C 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.25 (20972) covalent geometry : angle 0.82042 / 0.41 (31804) hydrogen bonds : bond 0.13198 / 7.92 ( 120) hydrogen bonds : angle 5.05851 / 2.68 ( 247) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 60 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 109 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6606 (mm) REVERT: C 172 THR cc_start: 0.8595 (p) cc_final: 0.8292 (p) REVERT: C 184 MET cc_start: 0.7614 (ptt) cc_final: 0.7193 (pmm) REVERT: C 223 ASN cc_start: 0.8825 (m110) cc_final: 0.8433 (p0) REVERT: C 225 TYR cc_start: 0.7055 (t80) cc_final: 0.6780 (t80) REVERT: C 386 LEU cc_start: 0.4624 (OUTLIER) cc_final: 0.4197 (pp) REVERT: C 412 TRP cc_start: 0.4694 (OUTLIER) cc_final: 0.4310 (m100) REVERT: C 481 MET cc_start: 0.5593 (mmt) cc_final: 0.5055 (mmm) REVERT: C 494 GLU cc_start: 0.2246 (OUTLIER) cc_final: 0.1271 (pm20) REVERT: C 500 GLN cc_start: 0.3532 (OUTLIER) cc_final: 0.3117 (tt0) outliers start: 28 outliers final: 17 residues processed: 81 average time/residue: 0.1416 time to fit residues: 17.6415 Evaluate side-chains 72 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 167 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 412 TRP Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 500 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 24 optimal weight: 20.0000 chunk 100 optimal weight: 0.0040 chunk 9 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 40 optimal weight: 30.0000 chunk 6 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 overall best weight: 3.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 ASN C 349 HIS ** C 451 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 = 0.4459 r_free = 0.4459 target = 0.117128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.095544 restraints weight = 105105.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.098386 restraints weight = 50146.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.097924 restraints weight = 34627.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.098217 restraints weight = 28357.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.098447 restraints weight = 27152.358| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 1.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20972 Z= 0.207 Angle : 0.734 13.011 31804 Z= 0.373 Chirality : 0.038 0.233 4114 Planarity : 0.005 0.058 1389 Dihedral : 18.672 174.908 8969 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 24.12 Ramachandran Plot: Outliers : 0.84 % Allowed : 18.07 % Favored : 81.09 % Rotamer: Outliers : 6.12 % Allowed : 22.90 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 5.15 % Twisted Proline : 0.00 % 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: -4.88 (0.31), residues: 476 helix: -2.35 (0.39), residues: 132 sheet: -4.19 (1.16), residues: 10 loop : -3.91 (0.27), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 154 TYR 0.024 0.002 TYR C 442 PHE 0.021 0.002 PHE C 23 TRP 0.010 0.002 TRP C 412 HIS 0.009 0.002 HIS C 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.21 (20972) covalent geometry : angle 0.73412 / 0.37 (31804) hydrogen bonds : bond 0.11934 / 7.08 ( 120) hydrogen bonds : angle 4.74166 / 2.55 ( 247) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 56 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 109 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.6983 (mm) REVERT: C 184 MET cc_start: 0.7571 (ptt) cc_final: 0.7164 (pmm) REVERT: C 220 LEU cc_start: 0.8248 (mt) cc_final: 0.8029 (mt) REVERT: C 386 LEU cc_start: 0.4708 (OUTLIER) cc_final: 0.4283 (pp) REVERT: C 426 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7261 (mm) REVERT: C 481 MET cc_start: 0.5554 (mmt) cc_final: 0.5060 (mmm) outliers start: 27 outliers final: 20 residues processed: 78 average time/residue: 0.1475 time to fit residues: 17.4378 Evaluate side-chains 73 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 50 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 MET Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 167 ASN Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 466 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 35 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 74 optimal weight: 0.2980 chunk 63 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 84 optimal weight: 0.0870 chunk 10 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 overall best weight: 4.0764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.115760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.094139 restraints weight = 106289.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.096966 restraints weight = 51635.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.096661 restraints weight = 32390.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.096842 restraints weight = 26598.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.097065 restraints weight = 25394.438| |-----------------------------------------------------------------------------| r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 moved from start: 1.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20972 Z= 0.231 Angle : 0.779 12.994 31804 Z= 0.393 Chirality : 0.039 0.271 4114 Planarity : 0.006 0.059 1389 Dihedral : 18.909 177.594 8969 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 26.33 Ramachandran Plot: Outliers : 0.84 % Allowed : 20.80 % Favored : 78.36 % Rotamer: Outliers : 6.12 % Allowed : 24.26 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 5.15 % Twisted Proline : 0.00 % 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: -5.02 (0.30), residues: 476 helix: -2.40 (0.38), residues: 140 sheet: -4.33 (1.14), residues: 10 loop : -4.05 (0.26), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 531 TYR 0.019 0.002 TYR C 225 PHE 0.022 0.003 PHE C 23 TRP 0.012 0.002 TRP C 412 HIS 0.010 0.002 HIS C 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.23 (20972) covalent geometry : angle 0.77883 / 0.39 (31804) hydrogen bonds : bond 0.12458 / 7.43 ( 120) hydrogen bonds : angle 4.85005 / 2.52 ( 247) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 53 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 111 GLN cc_start: 0.7762 (tp-100) cc_final: 0.7490 (tp-100) REVERT: C 184 MET cc_start: 0.7501 (ptt) cc_final: 0.7146 (pmm) REVERT: C 223 ASN cc_start: 0.8812 (m110) cc_final: 0.8434 (p0) REVERT: C 386 LEU cc_start: 0.4807 (OUTLIER) cc_final: 0.4402 (pp) REVERT: C 426 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.6984 (mm) REVERT: C 481 MET cc_start: 0.5673 (mmt) cc_final: 0.5142 (mmm) REVERT: C 500 GLN cc_start: 0.3424 (OUTLIER) cc_final: 0.2933 (tt0) outliers start: 27 outliers final: 20 residues processed: 74 average time/residue: 0.1511 time to fit residues: 16.9323 Evaluate side-chains 73 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 50 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 MET Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 500 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 44 optimal weight: 50.0000 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 78 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 40 optimal weight: 30.0000 chunk 54 optimal weight: 20.0000 chunk 94 optimal weight: 0.4980 chunk 91 optimal weight: 0.0570 chunk 66 optimal weight: 50.0000 chunk 56 optimal weight: 20.0000 overall best weight: 2.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.117738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.096341 restraints weight = 101585.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.099291 restraints weight = 48080.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.099056 restraints weight = 29186.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.099203 restraints weight = 24304.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.099547 restraints weight = 21335.074| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 1.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20972 Z= 0.170 Angle : 0.683 12.871 31804 Z= 0.347 Chirality : 0.035 0.216 4114 Planarity : 0.005 0.055 1389 Dihedral : 18.630 179.379 8969 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 21.87 Ramachandran Plot: Outliers : 0.84 % Allowed : 17.86 % Favored : 81.30 % Rotamer: Outliers : 4.99 % Allowed : 25.17 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 5.15 % Twisted Proline : 0.00 % 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: -4.88 (0.31), residues: 476 helix: -2.18 (0.39), residues: 136 sheet: -3.93 (1.29), residues: 10 loop : -4.02 (0.27), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 537 TYR 0.016 0.002 TYR C 442 PHE 0.022 0.002 PHE C 23 TRP 0.013 0.002 TRP C 202 HIS 0.010 0.002 HIS C 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.17 (20972) covalent geometry : angle 0.68300 / 0.35 (31804) hydrogen bonds : bond 0.10432 / 6.18 ( 120) hydrogen bonds : angle 4.46608 / 2.38 ( 247) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 111 GLN cc_start: 0.7733 (tp-100) cc_final: 0.7411 (tp-100) REVERT: C 184 MET cc_start: 0.7412 (ptt) cc_final: 0.6995 (pmm) REVERT: C 225 TYR cc_start: 0.7059 (t80) cc_final: 0.6854 (t80) REVERT: C 333 HIS cc_start: 0.8168 (OUTLIER) cc_final: 0.7374 (t70) REVERT: C 386 LEU cc_start: 0.4721 (OUTLIER) cc_final: 0.4339 (pp) REVERT: C 426 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7586 (mm) REVERT: C 481 MET cc_start: 0.5747 (mmt) cc_final: 0.5248 (mmm) REVERT: C 500 GLN cc_start: 0.3311 (OUTLIER) cc_final: 0.2743 (tt0) outliers start: 22 outliers final: 17 residues processed: 74 average time/residue: 0.1442 time to fit residues: 16.4577 Evaluate side-chains 73 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 167 ASN Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 333 HIS Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 500 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 105 optimal weight: 0.7980 chunk 99 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 84 optimal weight: 0.4980 chunk 58 optimal weight: 20.0000 chunk 89 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 overall best weight: 4.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.115887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.094301 restraints weight = 103155.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.097054 restraints weight = 49174.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.096773 restraints weight = 32938.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.097214 restraints weight = 25835.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.097329 restraints weight = 23998.733| |-----------------------------------------------------------------------------| r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 1.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20972 Z= 0.227 Angle : 0.768 13.998 31804 Z= 0.386 Chirality : 0.038 0.248 4114 Planarity : 0.005 0.055 1389 Dihedral : 18.962 178.934 8969 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 25.39 Ramachandran Plot: Outliers : 0.84 % Allowed : 20.80 % Favored : 78.36 % Rotamer: Outliers : 5.44 % Allowed : 25.62 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 5.15 % Twisted Proline : 0.00 % 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: -4.95 (0.30), residues: 476 helix: -2.23 (0.39), residues: 139 sheet: -4.15 (1.12), residues: 10 loop : -4.07 (0.26), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 537 TYR 0.023 0.002 TYR C 225 PHE 0.024 0.003 PHE C 23 TRP 0.012 0.002 TRP C 202 HIS 0.010 0.002 HIS C 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.23 (20972) covalent geometry : angle 0.76780 / 0.39 (31804) hydrogen bonds : bond 0.11860 / 7.10 ( 120) hydrogen bonds : angle 4.75441 / 2.50 ( 247) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 54 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 184 MET cc_start: 0.7575 (ptt) cc_final: 0.7237 (pmm) REVERT: C 186 MET cc_start: 0.7278 (mtm) cc_final: 0.6365 (tpt) REVERT: C 223 ASN cc_start: 0.8850 (m110) cc_final: 0.8421 (p0) REVERT: C 386 LEU cc_start: 0.4859 (OUTLIER) cc_final: 0.4465 (pp) REVERT: C 413 PHE cc_start: 0.5616 (OUTLIER) cc_final: 0.4558 (t80) REVERT: C 426 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7281 (mm) REVERT: C 481 MET cc_start: 0.5681 (mmt) cc_final: 0.5155 (mmm) REVERT: C 500 GLN cc_start: 0.3362 (OUTLIER) cc_final: 0.2844 (tt0) outliers start: 24 outliers final: 20 residues processed: 73 average time/residue: 0.1488 time to fit residues: 16.5135 Evaluate side-chains 77 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 53 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 MET Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 167 ASN Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 337 LYS Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 500 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 2 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 64 optimal weight: 20.0000 chunk 105 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.114496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.093233 restraints weight = 106416.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.094878 restraints weight = 54653.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.095510 restraints weight = 40188.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.095384 restraints weight = 36769.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.095572 restraints weight = 28613.099| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 1.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 20972 Z= 0.279 Angle : 0.851 14.340 31804 Z= 0.428 Chirality : 0.043 0.540 4114 Planarity : 0.006 0.058 1389 Dihedral : 19.415 179.043 8969 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 29.39 Ramachandran Plot: Outliers : 0.84 % Allowed : 20.59 % Favored : 78.57 % Rotamer: Outliers : 5.44 % Allowed : 24.26 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 5.15 % Twisted Proline : 0.00 % 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: -4.91 (0.30), residues: 476 helix: -2.14 (0.40), residues: 128 sheet: -4.07 (1.14), residues: 10 loop : -4.03 (0.26), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 537 TYR 0.025 0.003 TYR C 225 PHE 0.024 0.003 PHE C 23 TRP 0.014 0.003 TRP C 412 HIS 0.011 0.002 HIS C 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.28 (20972) covalent geometry : angle 0.85113 / 0.43 (31804) hydrogen bonds : bond 0.13262 / 7.97 ( 120) hydrogen bonds : angle 4.96276 / 2.56 ( 247) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3063.51 seconds wall clock time: 53 minutes 58.08 seconds (3238.08 seconds total)