Starting phenix.real_space_refine on Sun Aug 24 08:26:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5g2x_3331/08_2025/5g2x_3331.cif Found real_map, /net/cci-nas-00/data/ceres_data/5g2x_3331/08_2025/5g2x_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/5g2x_3331/08_2025/5g2x_3331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5g2x_3331/08_2025/5g2x_3331.map" model { file = "/net/cci-nas-00/data/ceres_data/5g2x_3331/08_2025/5g2x_3331.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5g2x_3331/08_2025/5g2x_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 4.01, per 1000 atoms: 0.21 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: 1.68 Conformation dependent library (CDL) restraints added in 287.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.31 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: 3.73 Time building geometry restraints manager: 2.28 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: 11728 35.59 - 71.19: 1197 71.19 - 106.78: 151 106.78 - 142.37: 3 142.37 - 177.96: 8 Dihedral angle restraints: 13087 sinusoidal: 11659 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 13084 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: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.610 Find NCS groups from input model: 0.060 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: 20.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2869 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 : 21.034 177.965 12169 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 aren 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 covalent geometry : bond 0.00137 (20972) covalent geometry : angle 0.32118 (31804) hydrogen bonds : bond 0.32553 ( 120) hydrogen bonds : angle 12.98927 ( 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 : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 481 MET cc_start: 0.5011 (mmt) cc_final: 0.4803 (mmm) outliers start: 2 outliers final: 1 residues processed: 124 average time/residue: 0.1721 time to fit residues: 30.7719 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 : 0.246 ------------------------------------------------------------------------------- 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: 9.9990 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: 9.9990 chunk 65 optimal weight: 40.0000 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 = 0.4576 r_free = 0.4576 target = 0.127609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.109589 restraints weight = 115639.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.110145 restraints weight = 66059.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.111026 restraints weight = 44807.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.111075 restraints weight = 33735.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.111153 restraints weight = 34157.779| |-----------------------------------------------------------------------------| r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6120 moved from start: 0.6434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 20972 Z= 0.403 Angle : 1.153 13.193 31804 Z= 0.561 Chirality : 0.052 0.290 4114 Planarity : 0.008 0.071 1389 Dihedral : 23.488 179.618 11149 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 31.21 Ramachandran Plot: Outliers : 1.26 % Allowed : 19.12 % Favored : 79.62 % Rotamer: Outliers : 4.31 % Allowed : 12.02 % Favored : 83.67 % 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 aren not related in a simple way. whole: -5.25 (0.30), residues: 476 helix: -3.15 (0.32), residues: 131 sheet: None (None), residues: 0 loop : -3.97 (0.28), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG C 115 TYR 0.034 0.005 TYR C 303 PHE 0.031 0.004 PHE C 310 TRP 0.020 0.003 TRP C 412 HIS 0.013 0.003 HIS C 140 Details of bonding type rmsd covalent geometry : bond 0.00757 (20972) covalent geometry : angle 1.15336 (31804) hydrogen bonds : bond 0.16954 ( 120) hydrogen bonds : angle 5.10458 ( 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 96 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 155 TRP cc_start: 0.3946 (m-10) cc_final: 0.3621 (m-10) REVERT: C 305 ARG cc_start: 0.6206 (ptt90) cc_final: 0.5399 (ptt90) REVERT: C 342 GLU cc_start: 0.5981 (pm20) cc_final: 0.5633 (pm20) REVERT: C 479 ILE cc_start: 0.7270 (mt) cc_final: 0.7008 (mm) REVERT: C 499 LYS cc_start: 0.3376 (OUTLIER) cc_final: 0.1368 (tttt) outliers start: 19 outliers final: 6 residues processed: 93 average time/residue: 0.1405 time to fit residues: 19.6782 Evaluate side-chains 60 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 102 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 chunk 62 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 93 ASN ** C 167 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.127794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.109814 restraints weight = 117119.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.111238 restraints weight = 69133.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.111049 restraints weight = 49887.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.111311 restraints weight = 46302.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.111322 restraints weight = 41633.002| |-----------------------------------------------------------------------------| r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6094 moved from start: 0.6910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20972 Z= 0.189 Angle : 0.697 12.908 31804 Z= 0.351 Chirality : 0.035 0.196 4114 Planarity : 0.005 0.050 1389 Dihedral : 23.414 172.270 11147 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 1.05 % Allowed : 18.49 % Favored : 80.46 % Rotamer: Outliers : 3.63 % Allowed : 17.01 % Favored : 79.37 % 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 aren not related in a simple way. whole: -4.75 (0.32), residues: 476 helix: -2.23 (0.42), residues: 124 sheet: None (None), residues: 0 loop : -3.86 (0.28), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 502 TYR 0.027 0.002 TYR C 36 PHE 0.017 0.002 PHE C 310 TRP 0.005 0.001 TRP C 412 HIS 0.009 0.001 HIS C 349 Details of bonding type rmsd covalent geometry : bond 0.00357 (20972) covalent geometry : angle 0.69742 (31804) hydrogen bonds : bond 0.10701 ( 120) hydrogen bonds : angle 4.21559 ( 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 74 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 97 MET cc_start: 0.3279 (mmp) cc_final: 0.2859 (mmm) REVERT: C 342 GLU cc_start: 0.6218 (pm20) cc_final: 0.5918 (pm20) outliers start: 16 outliers final: 8 residues processed: 72 average time/residue: 0.1199 time to fit residues: 14.4275 Evaluate side-chains 53 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 384 VAL 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: 9.9990 chunk 90 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 104 optimal weight: 0.7980 chunk 63 optimal weight: 9.9990 chunk 67 optimal weight: 40.0000 chunk 111 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 105 optimal weight: 4.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 GLN ** C 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.116520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.096235 restraints weight = 105331.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.097124 restraints weight = 54858.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.097160 restraints weight = 44097.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.097371 restraints weight = 39726.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.097476 restraints weight = 35282.167| |-----------------------------------------------------------------------------| r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 moved from start: 0.9597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 20972 Z= 0.338 Angle : 1.002 13.046 31804 Z= 0.502 Chirality : 0.048 0.309 4114 Planarity : 0.007 0.100 1389 Dihedral : 24.598 172.947 11147 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 33.23 Ramachandran Plot: Outliers : 1.26 % Allowed : 19.75 % Favored : 78.99 % Rotamer: Outliers : 6.35 % Allowed : 18.82 % Favored : 74.83 % 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 aren not related in a simple way. whole: -5.30 (0.29), residues: 476 helix: -2.81 (0.35), residues: 138 sheet: None (None), residues: 0 loop : -4.19 (0.26), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 355 TYR 0.043 0.004 TYR C 225 PHE 0.040 0.004 PHE C 62 TRP 0.011 0.003 TRP C 202 HIS 0.013 0.002 HIS C 170 Details of bonding type rmsd covalent geometry : bond 0.00633 (20972) covalent geometry : angle 1.00203 (31804) hydrogen bonds : bond 0.15576 ( 120) hydrogen bonds : angle 5.52947 ( 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 92 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 64 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 97 MET cc_start: 0.3574 (mmp) cc_final: 0.3350 (mmm) REVERT: C 386 LEU cc_start: 0.5267 (OUTLIER) cc_final: 0.5011 (pp) REVERT: C 500 GLN cc_start: 0.3598 (OUTLIER) cc_final: 0.3167 (tt0) outliers start: 28 outliers final: 18 residues processed: 83 average time/residue: 0.1256 time to fit residues: 16.3375 Evaluate side-chains 73 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 67 ILE Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 167 ASN Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 221 LEU 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 379 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 406 GLN Chi-restraints excluded: chain C residue 500 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 109 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 8 optimal weight: 20.0000 chunk 41 optimal weight: 50.0000 chunk 50 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 overall best weight: 4.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 406 GLN ** 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 = 0.4454 r_free = 0.4454 target = 0.117073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.095429 restraints weight = 103793.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.098188 restraints weight = 49074.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.098167 restraints weight = 29241.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.098287 restraints weight = 25020.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.098591 restraints weight = 23746.316| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 moved from start: 1.0125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20972 Z= 0.262 Angle : 0.808 13.122 31804 Z= 0.408 Chirality : 0.041 0.255 4114 Planarity : 0.006 0.062 1389 Dihedral : 24.659 175.693 11147 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 26.46 Ramachandran Plot: Outliers : 1.05 % Allowed : 18.07 % Favored : 80.88 % Rotamer: Outliers : 6.80 % Allowed : 20.63 % Favored : 72.56 % 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 aren not related in a simple way. whole: -4.92 (0.32), residues: 476 helix: -2.46 (0.39), residues: 129 sheet: -4.22 (1.53), residues: 10 loop : -3.89 (0.28), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 355 TYR 0.021 0.003 TYR C 225 PHE 0.017 0.003 PHE C 356 TRP 0.013 0.003 TRP C 489 HIS 0.011 0.003 HIS C 170 Details of bonding type rmsd covalent geometry : bond 0.00499 (20972) covalent geometry : angle 0.80775 (31804) hydrogen bonds : bond 0.12625 ( 120) hydrogen bonds : angle 4.83501 ( 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 93 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 63 time to evaluate : 0.280 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 109 LEU cc_start: 0.6628 (mt) cc_final: 0.6420 (mm) REVERT: C 168 ILE cc_start: 0.7592 (mt) cc_final: 0.7352 (mt) REVERT: C 336 LEU cc_start: 0.8382 (tp) cc_final: 0.8139 (tt) REVERT: C 386 LEU cc_start: 0.5222 (OUTLIER) cc_final: 0.4746 (pp) REVERT: C 494 GLU cc_start: 0.1655 (OUTLIER) cc_final: 0.0670 (pm20) outliers start: 30 outliers final: 18 residues processed: 86 average time/residue: 0.1358 time to fit residues: 18.0681 Evaluate side-chains 74 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 65 GLU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 321 CYS 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 384 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 393 LYS 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: 1.9990 chunk 24 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.116785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.096254 restraints weight = 107647.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.097469 restraints weight = 58542.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.097978 restraints weight = 38606.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.097864 restraints weight = 37126.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.097951 restraints weight = 32413.785| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 1.0699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20972 Z= 0.237 Angle : 0.783 13.023 31804 Z= 0.398 Chirality : 0.040 0.243 4114 Planarity : 0.006 0.056 1389 Dihedral : 24.694 175.114 11147 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 26.39 Ramachandran Plot: Outliers : 0.84 % Allowed : 17.65 % Favored : 81.51 % 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 aren not related in a simple way. whole: -4.98 (0.31), residues: 476 helix: -2.55 (0.37), residues: 141 sheet: None (None), residues: 0 loop : -3.99 (0.28), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 437 TYR 0.024 0.003 TYR C 442 PHE 0.025 0.003 PHE C 23 TRP 0.012 0.002 TRP C 323 HIS 0.009 0.002 HIS C 170 Details of bonding type rmsd covalent geometry : bond 0.00446 (20972) covalent geometry : angle 0.78328 (31804) hydrogen bonds : bond 0.12653 ( 120) hydrogen bonds : angle 4.72224 ( 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 84 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 56 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 111 GLN cc_start: 0.8067 (tp-100) cc_final: 0.7793 (tp-100) REVERT: C 184 MET cc_start: 0.7439 (ptt) cc_final: 0.6982 (pmm) REVERT: C 223 ASN cc_start: 0.8642 (m110) cc_final: 0.8309 (p0) REVERT: C 338 MET cc_start: 0.2773 (ttt) cc_final: 0.2546 (ttp) REVERT: C 386 LEU cc_start: 0.4844 (OUTLIER) cc_final: 0.4522 (pp) REVERT: C 426 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7252 (mm) REVERT: C 481 MET cc_start: 0.5892 (mmt) cc_final: 0.5373 (mmm) REVERT: C 494 GLU cc_start: 0.2259 (OUTLIER) cc_final: 0.1304 (pm20) REVERT: C 500 GLN cc_start: 0.3171 (OUTLIER) cc_final: 0.2707 (tt0) outliers start: 28 outliers final: 18 residues processed: 78 average time/residue: 0.1307 time to fit residues: 15.9391 Evaluate side-chains 73 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 51 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 65 GLU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 87 MET 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 172 THR Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 321 CYS 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 384 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 426 LEU 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: 0.8980 chunk 9 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 106 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 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: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.117287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.095976 restraints weight = 106719.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.098543 restraints weight = 52588.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.098322 restraints weight = 35565.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.098512 restraints weight = 28763.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.098607 restraints weight = 27268.856| |-----------------------------------------------------------------------------| r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6424 moved from start: 1.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20972 Z= 0.211 Angle : 0.729 13.034 31804 Z= 0.371 Chirality : 0.038 0.240 4114 Planarity : 0.005 0.057 1389 Dihedral : 24.666 175.110 11147 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 24.64 Ramachandran Plot: Outliers : 0.84 % Allowed : 17.02 % Favored : 82.14 % Rotamer: Outliers : 6.35 % Allowed : 21.54 % Favored : 72.11 % 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 aren not related in a simple way. whole: -4.80 (0.33), residues: 476 helix: -2.32 (0.38), residues: 143 sheet: -4.34 (1.33), residues: 10 loop : -3.87 (0.29), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 355 TYR 0.020 0.002 TYR C 529 PHE 0.016 0.002 PHE C 165 TRP 0.010 0.002 TRP C 323 HIS 0.010 0.002 HIS C 170 Details of bonding type rmsd covalent geometry : bond 0.00396 (20972) covalent geometry : angle 0.72914 (31804) hydrogen bonds : bond 0.11597 ( 120) hydrogen bonds : angle 4.55970 ( 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 85 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 57 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 111 GLN cc_start: 0.7944 (tp-100) cc_final: 0.7623 (tp40) REVERT: C 184 MET cc_start: 0.7484 (ptt) cc_final: 0.7145 (pmm) REVERT: C 319 GLU cc_start: 0.6219 (OUTLIER) cc_final: 0.5959 (tp30) REVERT: C 386 LEU cc_start: 0.4967 (OUTLIER) cc_final: 0.4645 (pp) REVERT: C 426 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7615 (mm) REVERT: C 494 GLU cc_start: 0.2078 (OUTLIER) cc_final: 0.1059 (pm20) REVERT: C 500 GLN cc_start: 0.3111 (OUTLIER) cc_final: 0.2652 (tt0) outliers start: 28 outliers final: 21 residues processed: 81 average time/residue: 0.1511 time to fit residues: 18.8376 Evaluate side-chains 76 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 50 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 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 141 THR Chi-restraints excluded: chain C residue 143 LEU 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 319 GLU Chi-restraints excluded: chain C residue 321 CYS 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 424 THR Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 452 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 35 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 107 optimal weight: 0.6980 chunk 84 optimal weight: 0.0970 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: 10.0000 overall best weight: 3.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.116749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.095555 restraints weight = 105760.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.097829 restraints weight = 51749.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.097874 restraints weight = 32275.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.098156 restraints weight = 27059.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.098312 restraints weight = 26038.209| |-----------------------------------------------------------------------------| r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 1.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20972 Z= 0.209 Angle : 0.733 12.981 31804 Z= 0.373 Chirality : 0.038 0.236 4114 Planarity : 0.006 0.058 1389 Dihedral : 24.707 178.992 11147 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 24.83 Ramachandran Plot: Outliers : 0.84 % Allowed : 18.49 % Favored : 80.67 % Rotamer: Outliers : 6.58 % Allowed : 23.36 % Favored : 70.07 % 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 aren not related in a simple way. whole: -4.67 (0.33), residues: 476 helix: -2.23 (0.38), residues: 137 sheet: -4.47 (1.24), residues: 10 loop : -3.74 (0.29), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 32 TYR 0.015 0.002 TYR C 442 PHE 0.026 0.003 PHE C 23 TRP 0.025 0.003 TRP C 323 HIS 0.010 0.002 HIS C 349 Details of bonding type rmsd covalent geometry : bond 0.00394 (20972) covalent geometry : angle 0.73303 (31804) hydrogen bonds : bond 0.11532 ( 120) hydrogen bonds : angle 4.66291 ( 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 83 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 54 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 111 GLN cc_start: 0.8156 (tp-100) cc_final: 0.7913 (tp-100) REVERT: C 134 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.6845 (mmm160) REVERT: C 184 MET cc_start: 0.7622 (ptt) cc_final: 0.6917 (pmm) REVERT: C 223 ASN cc_start: 0.8841 (m110) cc_final: 0.8427 (p0) REVERT: C 386 LEU cc_start: 0.5016 (OUTLIER) cc_final: 0.4705 (pp) REVERT: C 426 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7295 (mm) REVERT: C 481 MET cc_start: 0.5643 (mmt) cc_final: 0.5234 (mmm) REVERT: C 494 GLU cc_start: 0.2163 (OUTLIER) cc_final: 0.1260 (pm20) REVERT: C 500 GLN cc_start: 0.3188 (OUTLIER) cc_final: 0.2708 (tt0) outliers start: 29 outliers final: 23 residues processed: 73 average time/residue: 0.1598 time to fit residues: 17.8343 Evaluate side-chains 78 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 50 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 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 125 VAL Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 143 LEU 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 321 CYS 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 403 ILE Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 452 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 44 optimal weight: 50.0000 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 40 optimal weight: 30.0000 chunk 54 optimal weight: 20.0000 chunk 94 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 66 optimal weight: 50.0000 chunk 56 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.114367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.092745 restraints weight = 106933.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.095160 restraints weight = 52476.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.095078 restraints weight = 32957.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.095315 restraints weight = 29491.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.095749 restraints weight = 25586.056| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 1.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 20972 Z= 0.289 Angle : 0.873 13.083 31804 Z= 0.439 Chirality : 0.043 0.268 4114 Planarity : 0.006 0.061 1389 Dihedral : 25.135 179.994 11147 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 30.50 Ramachandran Plot: Outliers : 1.26 % Allowed : 19.96 % Favored : 78.78 % Rotamer: Outliers : 6.80 % Allowed : 22.45 % Favored : 70.75 % 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 aren not related in a simple way. whole: -4.91 (0.31), residues: 476 helix: -2.36 (0.37), residues: 135 sheet: -4.63 (1.11), residues: 10 loop : -3.93 (0.29), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 32 TYR 0.018 0.003 TYR C 529 PHE 0.027 0.003 PHE C 23 TRP 0.015 0.003 TRP C 323 HIS 0.011 0.002 HIS C 349 Details of bonding type rmsd covalent geometry : bond 0.00548 (20972) covalent geometry : angle 0.87322 (31804) hydrogen bonds : bond 0.13812 ( 120) hydrogen bonds : angle 5.19702 ( 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 81 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 51 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 PHE cc_start: 0.6542 (t80) cc_final: 0.6184 (t80) REVERT: C 115 ARG cc_start: 0.6975 (mmm160) cc_final: 0.6774 (mmm160) REVERT: C 134 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.6408 (mmm160) REVERT: C 184 MET cc_start: 0.7716 (ptt) cc_final: 0.7021 (pmm) REVERT: C 223 ASN cc_start: 0.8879 (m110) cc_final: 0.8519 (p0) REVERT: C 333 HIS cc_start: 0.8109 (OUTLIER) cc_final: 0.7313 (t70) REVERT: C 386 LEU cc_start: 0.4965 (OUTLIER) cc_final: 0.4563 (pp) REVERT: C 413 PHE cc_start: 0.5607 (OUTLIER) cc_final: 0.5282 (t80) REVERT: C 426 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7280 (mm) REVERT: C 481 MET cc_start: 0.5668 (mmt) cc_final: 0.5255 (mmm) REVERT: C 494 GLU cc_start: 0.2485 (OUTLIER) cc_final: 0.1619 (pm20) REVERT: C 500 GLN cc_start: 0.3128 (OUTLIER) cc_final: 0.2681 (tt0) outliers start: 30 outliers final: 23 residues processed: 72 average time/residue: 0.1560 time to fit residues: 17.4125 Evaluate side-chains 78 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 48 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 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 125 VAL Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 143 LEU 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 321 CYS 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 333 HIS Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 452 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 105 optimal weight: 0.3980 chunk 99 optimal weight: 0.6980 chunk 3 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 58 optimal weight: 20.0000 chunk 89 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 GLN ** C 167 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.123291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.104980 restraints weight = 114176.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.106277 restraints weight = 61997.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.106106 restraints weight = 44993.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.106445 restraints weight = 45017.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.106446 restraints weight = 39921.511| |-----------------------------------------------------------------------------| r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6231 moved from start: 1.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 20972 Z= 0.130 Angle : 0.640 12.838 31804 Z= 0.327 Chirality : 0.033 0.219 4114 Planarity : 0.005 0.048 1389 Dihedral : 24.601 176.849 11147 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 1.05 % Allowed : 16.60 % Favored : 82.35 % Rotamer: Outliers : 4.08 % Allowed : 26.08 % 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 aren not related in a simple way. whole: -4.65 (0.32), residues: 476 helix: -2.14 (0.39), residues: 131 sheet: None (None), residues: 0 loop : -3.82 (0.28), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 531 TYR 0.019 0.002 TYR C 80 PHE 0.021 0.002 PHE C 23 TRP 0.013 0.002 TRP C 202 HIS 0.009 0.002 HIS C 349 Details of bonding type rmsd covalent geometry : bond 0.00248 (20972) covalent geometry : angle 0.63969 (31804) hydrogen bonds : bond 0.09372 ( 120) hydrogen bonds : angle 4.58389 ( 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 67 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 97 MET cc_start: 0.2738 (mmm) cc_final: 0.2537 (mmp) REVERT: C 134 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6347 (mmm160) REVERT: C 184 MET cc_start: 0.7157 (ptt) cc_final: 0.6653 (pmm) REVERT: C 223 ASN cc_start: 0.8795 (m110) cc_final: 0.8502 (p0) REVERT: C 386 LEU cc_start: 0.5011 (OUTLIER) cc_final: 0.4578 (pp) REVERT: C 426 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7590 (mm) REVERT: C 481 MET cc_start: 0.6042 (mmt) cc_final: 0.5675 (mmt) outliers start: 18 outliers final: 14 residues processed: 61 average time/residue: 0.1580 time to fit residues: 14.8571 Evaluate side-chains 64 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 ILE 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 125 VAL Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 141 THR 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 321 CYS 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=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: 3.9990 chunk 61 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 overall best weight: 4.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.115414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.095098 restraints weight = 108494.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.096377 restraints weight = 57777.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.097101 restraints weight = 46581.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.097093 restraints weight = 39826.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.097082 restraints weight = 31953.621| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6429 moved from start: 1.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 20972 Z= 0.263 Angle : 0.819 13.029 31804 Z= 0.412 Chirality : 0.040 0.263 4114 Planarity : 0.005 0.057 1389 Dihedral : 24.986 177.168 11147 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 27.11 Ramachandran Plot: Outliers : 1.05 % Allowed : 19.33 % Favored : 79.62 % Rotamer: Outliers : 5.22 % Allowed : 24.72 % Favored : 70.07 % 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 aren not related in a simple way. whole: -4.76 (0.32), residues: 476 helix: -2.27 (0.37), residues: 141 sheet: -4.63 (1.12), residues: 10 loop : -3.82 (0.30), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 32 TYR 0.031 0.003 TYR C 442 PHE 0.027 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 covalent geometry : bond 0.00497 (20972) covalent geometry : angle 0.81868 (31804) hydrogen bonds : bond 0.12364 ( 120) hydrogen bonds : angle 5.07927 ( 247) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3151.89 seconds wall clock time: 55 minutes 31.90 seconds (3331.90 seconds total)