Starting phenix.real_space_refine on Thu Jul 2 18:50:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wk0_32554/07_2026/7wk0_32554.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wk0_32554/07_2026/7wk0_32554.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7wk0_32554/07_2026/7wk0_32554.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wk0_32554/07_2026/7wk0_32554.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wk0_32554/07_2026/7wk0_32554.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wk0_32554/07_2026/7wk0_32554.map" model { file = "/net/cci-nas-00/data/ceres_data/7wk0_32554/07_2026/7wk0_32554.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wk0_32554/07_2026/7wk0_32554.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 6154 2.51 5 N 1646 2.21 5 O 1890 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9724 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1699 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 214} Chain: "B" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1577 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 16, 'TRANS': 193} Chain: "C" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1572 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 183} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1699 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 214} Chain: "E" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1577 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 16, 'TRANS': 193} Chain: "F" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1572 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 183} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.31, per 1000 atoms: 0.24 Number of scatterers: 9724 At special positions: 0 Unit cell: (88.312, 155.344, 110.656, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1890 8.00 N 1646 7.00 C 6154 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 87 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 153 " - pdb=" SG CYS D 209 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 87 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 195 " distance=2.04 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.03 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.03 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 Links applied NAG-ASN " NAG C 601 " - " ASN C 343 " " NAG F 601 " - " ASN F 343 " Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 387.4 milliseconds 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2328 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 25 sheets defined 2.2% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 87 through 91 removed outlier: 4.131A pdb=" N THR A 91 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 82 Processing helix chain 'B' and resid 123 through 127 removed outlier: 3.804A pdb=" N GLU B 126 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 127 " --> pdb=" O SER B 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 123 through 127' Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'E' and resid 78 through 82 removed outlier: 3.567A pdb=" N ASP E 81 " --> pdb=" O GLU E 78 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU E 82 " --> pdb=" O ALA E 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 78 through 82' Processing helix chain 'F' and resid 502 through 506 removed outlier: 3.798A pdb=" N GLN F 506 " --> pdb=" O VAL F 503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 60 removed outlier: 5.936A pdb=" N GLY A 50 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TYR A 60 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL A 48 " --> pdb=" O TYR A 60 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N TRP A 47 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ARG A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 92 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A 94 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 120 " --> pdb=" O TYR A 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 removed outlier: 3.873A pdb=" N GLY A 152 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 163 through 166 removed outlier: 3.507A pdb=" N THR A 164 " --> pdb=" O ASN A 212 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS A 209 " --> pdb=" O LYS A 222 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS A 222 " --> pdb=" O CYS A 209 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 220 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS A 213 " --> pdb=" O THR A 218 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 218 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 9 through 12 removed outlier: 3.868A pdb=" N VAL B 10 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR B 106 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 18 through 22 removed outlier: 3.747A pdb=" N ILE B 74 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B 20 " --> pdb=" O LEU B 72 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 117 through 120 removed outlier: 3.503A pdb=" N ILE B 138 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 176 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP B 140 " --> pdb=" O TYR B 174 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TYR B 174 " --> pdb=" O ASP B 140 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 155 through 156 removed outlier: 3.752A pdb=" N THR B 147 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS B 195 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS B 206 " --> pdb=" O CYS B 195 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.726A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.726A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.534A pdb=" N LEU D 18 " --> pdb=" O MET D 83 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.628A pdb=" N TYR D 94 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL D 48 " --> pdb=" O TYR D 60 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N TYR D 60 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLY D 50 " --> pdb=" O ILE D 58 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 151 through 153 removed outlier: 3.533A pdb=" N LEU D 151 " --> pdb=" O VAL D 195 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER D 193 " --> pdb=" O CYS D 153 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER D 192 " --> pdb=" O PHE D 179 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 208 through 211 Processing sheet with id=AB8, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.887A pdb=" N VAL E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AC1, first strand: chain 'E' and resid 44 through 47 removed outlier: 5.626A pdb=" N LEU E 45 " --> pdb=" O GLN E 36 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLN E 36 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL E 47 " --> pdb=" O TRP E 34 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 117 through 120 removed outlier: 3.899A pdb=" N VAL E 135 " --> pdb=" O PHE E 120 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE E 138 " --> pdb=" O ALA E 176 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASP E 140 " --> pdb=" O TYR E 174 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR E 174 " --> pdb=" O ASP E 140 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 194 through 196 removed outlier: 3.674A pdb=" N CYS E 195 " --> pdb=" O LYS E 206 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS E 206 " --> pdb=" O CYS E 195 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 357 through 358 removed outlier: 4.190A pdb=" N ASN F 394 " --> pdb=" O GLU F 516 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU F 516 " --> pdb=" O ASN F 394 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA F 435 " --> pdb=" O THR F 376 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 357 through 358 removed outlier: 4.190A pdb=" N ASN F 394 " --> pdb=" O GLU F 516 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU F 516 " --> pdb=" O ASN F 394 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'F' and resid 473 through 474 183 hydrogen bonds defined for protein. 447 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.46 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1593 1.31 - 1.44: 2884 1.44 - 1.56: 5469 1.56 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 9982 Sorted by residual: bond pdb=" CA LYS D 65 " pdb=" C LYS D 65 " ideal model delta sigma weight residual 1.524 1.445 0.079 1.31e-02 5.83e+03 3.62e+01 bond pdb=" N ASN C 448 " pdb=" CA ASN C 448 " ideal model delta sigma weight residual 1.455 1.397 0.059 1.25e-02 6.40e+03 2.19e+01 bond pdb=" N GLU F 406 " pdb=" CA GLU F 406 " ideal model delta sigma weight residual 1.457 1.405 0.052 1.16e-02 7.43e+03 2.02e+01 bond pdb=" C ILE C 358 " pdb=" O ILE C 358 " ideal model delta sigma weight residual 1.237 1.188 0.050 1.13e-02 7.83e+03 1.93e+01 bond pdb=" CA ASN C 354 " pdb=" C ASN C 354 " ideal model delta sigma weight residual 1.523 1.469 0.053 1.23e-02 6.61e+03 1.89e+01 ... (remaining 9977 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 13311 1.98 - 3.97: 256 3.97 - 5.95: 38 5.95 - 7.94: 6 7.94 - 9.92: 3 Bond angle restraints: 13614 Sorted by residual: angle pdb=" N ASN C 370 " pdb=" CA ASN C 370 " pdb=" C ASN C 370 " ideal model delta sigma weight residual 114.31 104.48 9.83 1.29e+00 6.01e-01 5.81e+01 angle pdb=" N VAL F 407 " pdb=" CA VAL F 407 " pdb=" C VAL F 407 " ideal model delta sigma weight residual 111.58 104.58 7.00 1.06e+00 8.90e-01 4.36e+01 angle pdb=" N GLY D 66 " pdb=" CA GLY D 66 " pdb=" C GLY D 66 " ideal model delta sigma weight residual 115.27 107.54 7.73 1.41e+00 5.03e-01 3.00e+01 angle pdb=" N ASN C 448 " pdb=" CA ASN C 448 " pdb=" C ASN C 448 " ideal model delta sigma weight residual 109.24 101.13 8.11 1.67e+00 3.59e-01 2.36e+01 angle pdb=" N SER C 359 " pdb=" CA SER C 359 " pdb=" C SER C 359 " ideal model delta sigma weight residual 108.74 114.66 -5.92 1.38e+00 5.25e-01 1.84e+01 ... (remaining 13609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 5536 17.71 - 35.42: 304 35.42 - 53.14: 45 53.14 - 70.85: 16 70.85 - 88.56: 1 Dihedral angle restraints: 5902 sinusoidal: 2246 harmonic: 3656 Sorted by residual: dihedral pdb=" CA ARG B 191 " pdb=" C ARG B 191 " pdb=" N SER B 192 " pdb=" CA SER B 192 " ideal model delta harmonic sigma weight residual 180.00 155.96 24.04 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" N ASN C 448 " pdb=" C ASN C 448 " pdb=" CA ASN C 448 " pdb=" CB ASN C 448 " ideal model delta harmonic sigma weight residual 122.80 111.49 11.31 0 2.50e+00 1.60e-01 2.05e+01 dihedral pdb=" CA GLU A 161 " pdb=" C GLU A 161 " pdb=" N PRO A 162 " pdb=" CA PRO A 162 " ideal model delta harmonic sigma weight residual 180.00 159.66 20.34 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 5899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1322 0.071 - 0.142: 169 0.142 - 0.212: 4 0.212 - 0.283: 2 0.283 - 0.354: 1 Chirality restraints: 1498 Sorted by residual: chirality pdb=" CA LYS D 65 " pdb=" N LYS D 65 " pdb=" C LYS D 65 " pdb=" CB LYS D 65 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA ASN F 448 " pdb=" N ASN F 448 " pdb=" C ASN F 448 " pdb=" CB ASN F 448 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ALA C 372 " pdb=" N ALA C 372 " pdb=" C ALA C 372 " pdb=" CB ALA C 372 " both_signs ideal model delta sigma weight residual False 2.48 2.27 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1495 not shown) Planarity restraints: 1766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 601 " 0.257 2.00e-02 2.50e+03 2.18e-01 5.92e+02 pdb=" C7 NAG F 601 " -0.066 2.00e-02 2.50e+03 pdb=" C8 NAG F 601 " 0.169 2.00e-02 2.50e+03 pdb=" N2 NAG F 601 " -0.371 2.00e-02 2.50e+03 pdb=" O7 NAG F 601 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 400 " -0.021 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C PHE C 400 " 0.075 2.00e-02 2.50e+03 pdb=" O PHE C 400 " -0.029 2.00e-02 2.50e+03 pdb=" N VAL C 401 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP C 353 " 0.017 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C TRP C 353 " -0.058 2.00e-02 2.50e+03 pdb=" O TRP C 353 " 0.022 2.00e-02 2.50e+03 pdb=" N ASN C 354 " 0.020 2.00e-02 2.50e+03 ... (remaining 1763 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1603 2.77 - 3.30: 9290 3.30 - 3.83: 15901 3.83 - 4.37: 18585 4.37 - 4.90: 31950 Nonbonded interactions: 77329 Sorted by model distance: nonbonded pdb=" OG SER E 62 " pdb=" OG1 THR E 73 " model vdw 2.233 3.040 nonbonded pdb=" OG SER B 64 " pdb=" OG1 THR B 71 " model vdw 2.263 3.040 nonbonded pdb=" OD2 ASP C 398 " pdb=" OH TYR C 423 " model vdw 2.272 3.040 nonbonded pdb=" OD2 ASP E 91 " pdb=" OG SER E 94 " model vdw 2.278 3.040 nonbonded pdb=" OE1 GLU E 126 " pdb=" OG1 THR E 133 " model vdw 2.286 3.040 ... (remaining 77324 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.710 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.190 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 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 : 0.004 0.079 10000 Z= 0.296 Angle : 0.664 9.922 13652 Z= 0.388 Chirality : 0.045 0.354 1498 Planarity : 0.007 0.218 1764 Dihedral : 11.039 88.559 3526 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.22 % Favored : 87.54 % Rotamer: Outliers : 7.71 % Allowed : 7.99 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.96 (0.20), residues: 1252 helix: -5.35 (0.10), residues: 70 sheet: -2.88 (0.22), residues: 452 loop : -3.46 (0.19), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 403 TYR 0.008 0.001 TYR A 112 PHE 0.008 0.001 PHE C 375 TRP 0.010 0.001 TRP A 167 HIS 0.002 0.001 HIS B 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.30 ( 9982) covalent geometry : angle 0.65482 / 0.39 (13614) SS BOND : bond 0.00214 / 0.16 ( 16) SS BOND : angle 0.46490 / 0.32 ( 32) hydrogen bonds : bond 0.28683 / 20.04 ( 174) hydrogen bonds : angle 11.39510 / 7.90 ( 447) link_NAG-ASN : bond 0.00447 / 0.23 ( 2) link_NAG-ASN : angle 5.34599 / 2.86 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 237 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 SER cc_start: 0.7978 (m) cc_final: 0.7616 (t) REVERT: A 154 LEU cc_start: 0.8591 (tp) cc_final: 0.8217 (tp) REVERT: B 21 THR cc_start: 0.8338 (p) cc_final: 0.8136 (t) REVERT: B 116 SER cc_start: 0.7575 (t) cc_final: 0.7274 (p) REVERT: C 346 ARG cc_start: 0.8549 (mtt-85) cc_final: 0.8251 (mtt90) REVERT: C 438 SER cc_start: 0.8294 (m) cc_final: 0.8077 (p) REVERT: C 445 VAL cc_start: 0.8333 (OUTLIER) cc_final: 0.8103 (p) REVERT: C 448 ASN cc_start: 0.7714 (OUTLIER) cc_final: 0.7424 (p0) REVERT: C 459 SER cc_start: 0.8501 (p) cc_final: 0.8280 (m) REVERT: C 467 ASP cc_start: 0.7055 (p0) cc_final: 0.6626 (p0) REVERT: C 508 TYR cc_start: 0.8308 (m-80) cc_final: 0.7897 (m-80) REVERT: D 25 SER cc_start: 0.8443 (t) cc_final: 0.8099 (p) REVERT: D 37 VAL cc_start: 0.8300 (OUTLIER) cc_final: 0.8025 (m) REVERT: D 70 ILE cc_start: 0.8809 (tt) cc_final: 0.8585 (tt) REVERT: D 126 SER cc_start: 0.8376 (m) cc_final: 0.8124 (p) REVERT: D 134 VAL cc_start: 0.8661 (t) cc_final: 0.8455 (m) REVERT: E 78 GLU cc_start: 0.7089 (pm20) cc_final: 0.6506 (pm20) REVERT: E 81 ASP cc_start: 0.8128 (t70) cc_final: 0.7921 (t70) REVERT: E 147 THR cc_start: 0.8027 (m) cc_final: 0.7546 (p) REVERT: F 355 ARG cc_start: 0.7473 (mtp85) cc_final: 0.7100 (mtp85) REVERT: F 362 VAL cc_start: 0.8501 (t) cc_final: 0.8069 (p) REVERT: F 375 PHE cc_start: 0.6981 (OUTLIER) cc_final: 0.6576 (m-10) REVERT: F 377 PHE cc_start: 0.7852 (t80) cc_final: 0.7636 (t80) REVERT: F 394 ASN cc_start: 0.7326 (m-40) cc_final: 0.6887 (m-40) REVERT: F 439 ASN cc_start: 0.8213 (t0) cc_final: 0.7927 (t0) REVERT: F 503 VAL cc_start: 0.8803 (p) cc_final: 0.8588 (t) REVERT: F 517 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6655 (tm) outliers start: 82 outliers final: 35 residues processed: 296 average time/residue: 0.1069 time to fit residues: 43.3612 Evaluate side-chains 250 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 210 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 405 ASP Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain F residue 441 LEU Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain F residue 474 GLN Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 517 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.0470 chunk 49 optimal weight: 0.1980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.4980 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.0970 chunk 123 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.2276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 GLN B 33 HIS B 88 GLN B 110 GLN B 128 GLN B 190 HIS C 409 GLN C 437 ASN C 448 ASN C 481 ASN D 3 GLN D 118 GLN E 33 HIS ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN E 110 GLN E 172 ASN F 394 ASN F 409 GLN F 448 ASN F 474 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.130197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.115064 restraints weight = 14772.178| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.39 r_work: 0.3346 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10000 Z= 0.147 Angle : 0.610 6.559 13652 Z= 0.313 Chirality : 0.045 0.218 1498 Planarity : 0.005 0.044 1764 Dihedral : 7.976 71.783 1475 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % Rotamer: Outliers : 5.73 % Allowed : 13.25 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.25 (0.21), residues: 1252 helix: -5.00 (0.31), residues: 56 sheet: -2.15 (0.24), residues: 410 loop : -3.19 (0.19), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 191 TYR 0.015 0.001 TYR D 95 PHE 0.022 0.001 PHE C 377 TRP 0.015 0.001 TRP F 436 HIS 0.002 0.001 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 9982) covalent geometry : angle 0.60356 / 0.31 (13614) SS BOND : bond 0.00427 / 0.26 ( 16) SS BOND : angle 1.10563 / 0.77 ( 32) hydrogen bonds : bond 0.04457 / 2.94 ( 174) hydrogen bonds : angle 7.55499 / 5.14 ( 447) link_NAG-ASN : bond 0.00240 / 0.12 ( 2) link_NAG-ASN : angle 3.71184 / 1.91 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 221 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 SER cc_start: 0.8142 (m) cc_final: 0.7839 (p) REVERT: A 55 SER cc_start: 0.8241 (m) cc_final: 0.7813 (t) REVERT: A 154 LEU cc_start: 0.8725 (tp) cc_final: 0.8375 (tp) REVERT: B 151 LYS cc_start: 0.7311 (ttmm) cc_final: 0.7035 (ttmm) REVERT: C 346 ARG cc_start: 0.8705 (mtt-85) cc_final: 0.8435 (mtt90) REVERT: C 354 ASN cc_start: 0.8471 (t0) cc_final: 0.8191 (t0) REVERT: C 355 ARG cc_start: 0.8091 (ttt90) cc_final: 0.7781 (ttm170) REVERT: C 360 ASN cc_start: 0.8246 (m110) cc_final: 0.7904 (t0) REVERT: C 454 ARG cc_start: 0.8401 (ttm-80) cc_final: 0.8136 (ttm-80) REVERT: C 467 ASP cc_start: 0.7532 (p0) cc_final: 0.6905 (p0) REVERT: C 481 ASN cc_start: 0.8410 (m-40) cc_final: 0.8166 (m110) REVERT: C 508 TYR cc_start: 0.8645 (m-80) cc_final: 0.8392 (m-80) REVERT: D 25 SER cc_start: 0.8767 (t) cc_final: 0.8428 (p) REVERT: D 37 VAL cc_start: 0.8452 (OUTLIER) cc_final: 0.8177 (m) REVERT: D 126 SER cc_start: 0.8624 (m) cc_final: 0.8345 (p) REVERT: D 134 VAL cc_start: 0.8884 (t) cc_final: 0.8664 (m) REVERT: E 77 VAL cc_start: 0.7528 (OUTLIER) cc_final: 0.7302 (m) REVERT: E 78 GLU cc_start: 0.7817 (pm20) cc_final: 0.7230 (pm20) REVERT: E 81 ASP cc_start: 0.8488 (t70) cc_final: 0.8163 (t70) REVERT: E 119 LEU cc_start: 0.6811 (mm) cc_final: 0.6606 (tp) REVERT: E 147 THR cc_start: 0.8294 (m) cc_final: 0.7813 (p) REVERT: F 357 ARG cc_start: 0.8028 (mtp-110) cc_final: 0.7633 (mtp-110) REVERT: F 362 VAL cc_start: 0.8558 (t) cc_final: 0.8236 (p) REVERT: F 386 LYS cc_start: 0.8301 (mmtt) cc_final: 0.8027 (mmtt) REVERT: F 394 ASN cc_start: 0.7920 (m110) cc_final: 0.7349 (m110) REVERT: F 403 ARG cc_start: 0.7384 (mtm-85) cc_final: 0.7057 (mtm-85) REVERT: F 503 VAL cc_start: 0.8886 (p) cc_final: 0.8656 (t) REVERT: F 517 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7334 (tp) outliers start: 61 outliers final: 38 residues processed: 266 average time/residue: 0.1094 time to fit residues: 39.8199 Evaluate side-chains 239 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 517 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 84 optimal weight: 0.0370 chunk 120 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 99 optimal weight: 0.0040 chunk 91 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 64 optimal weight: 0.0070 chunk 24 optimal weight: 0.3980 overall best weight: 0.2088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 ASN A 168 ASN A 177 HIS B 190 HIS ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.128849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.113694 restraints weight = 14967.052| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.35 r_work: 0.3318 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10000 Z= 0.135 Angle : 0.592 7.289 13652 Z= 0.301 Chirality : 0.044 0.213 1498 Planarity : 0.004 0.042 1764 Dihedral : 7.386 73.070 1446 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % Rotamer: Outliers : 5.73 % Allowed : 15.70 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.80 (0.22), residues: 1252 helix: -5.02 (0.25), residues: 56 sheet: -1.80 (0.26), residues: 394 loop : -2.87 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 191 TYR 0.012 0.001 TYR D 95 PHE 0.023 0.001 PHE C 377 TRP 0.014 0.001 TRP F 436 HIS 0.004 0.001 HIS B 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 9982) covalent geometry : angle 0.58719 / 0.30 (13614) SS BOND : bond 0.00369 / 0.25 ( 16) SS BOND : angle 0.88428 / 0.61 ( 32) hydrogen bonds : bond 0.03795 / 2.44 ( 174) hydrogen bonds : angle 6.93892 / 4.71 ( 447) link_NAG-ASN : bond 0.00230 / 0.11 ( 2) link_NAG-ASN : angle 3.18994 / 1.65 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 193 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 17 SER cc_start: 0.8059 (m) cc_final: 0.7789 (p) REVERT: A 55 SER cc_start: 0.8226 (m) cc_final: 0.7786 (t) REVERT: A 85 SER cc_start: 0.8554 (t) cc_final: 0.8225 (t) REVERT: A 154 LEU cc_start: 0.8707 (tp) cc_final: 0.8349 (tp) REVERT: B 6 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7173 (mt0) REVERT: B 14 PRO cc_start: 0.8434 (Cg_endo) cc_final: 0.8140 (Cg_exo) REVERT: B 55 SER cc_start: 0.8003 (t) cc_final: 0.7627 (m) REVERT: C 346 ARG cc_start: 0.8679 (mtt-85) cc_final: 0.8437 (mtt90) REVERT: C 354 ASN cc_start: 0.8429 (t0) cc_final: 0.8227 (t0) REVERT: C 355 ARG cc_start: 0.8082 (ttt90) cc_final: 0.7788 (ttm170) REVERT: C 360 ASN cc_start: 0.8264 (m110) cc_final: 0.7897 (t0) REVERT: C 448 ASN cc_start: 0.7805 (p0) cc_final: 0.7471 (p0) REVERT: C 454 ARG cc_start: 0.8376 (ttm-80) cc_final: 0.8133 (ttm-80) REVERT: C 467 ASP cc_start: 0.7462 (p0) cc_final: 0.6850 (p0) REVERT: C 481 ASN cc_start: 0.8450 (m-40) cc_final: 0.8204 (m110) REVERT: C 488 CYS cc_start: 0.7286 (m) cc_final: 0.6853 (m) REVERT: C 508 TYR cc_start: 0.8623 (m-80) cc_final: 0.8340 (m-80) REVERT: C 509 ARG cc_start: 0.8865 (mtt-85) cc_final: 0.8561 (mtt180) REVERT: C 511 VAL cc_start: 0.8726 (OUTLIER) cc_final: 0.8408 (t) REVERT: D 25 SER cc_start: 0.8741 (t) cc_final: 0.8394 (p) REVERT: D 37 VAL cc_start: 0.8402 (OUTLIER) cc_final: 0.8148 (m) REVERT: D 93 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7803 (tt) REVERT: D 126 SER cc_start: 0.8645 (m) cc_final: 0.8341 (p) REVERT: D 134 VAL cc_start: 0.8870 (t) cc_final: 0.8647 (m) REVERT: E 71 THR cc_start: 0.8302 (m) cc_final: 0.7932 (t) REVERT: E 77 VAL cc_start: 0.7546 (OUTLIER) cc_final: 0.7307 (m) REVERT: E 78 GLU cc_start: 0.7833 (pm20) cc_final: 0.7315 (pm20) REVERT: E 81 ASP cc_start: 0.8445 (t70) cc_final: 0.8122 (t70) REVERT: F 354 ASN cc_start: 0.8058 (t0) cc_final: 0.7732 (t0) REVERT: F 362 VAL cc_start: 0.8544 (t) cc_final: 0.8236 (p) REVERT: F 386 LYS cc_start: 0.8331 (mmtt) cc_final: 0.8083 (mmtt) REVERT: F 439 ASN cc_start: 0.8456 (t0) cc_final: 0.8164 (t0) REVERT: F 503 VAL cc_start: 0.8911 (p) cc_final: 0.8684 (t) REVERT: F 517 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7351 (tp) outliers start: 61 outliers final: 41 residues processed: 238 average time/residue: 0.1083 time to fit residues: 35.3812 Evaluate side-chains 234 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 187 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 517 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.0980 chunk 22 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 ASN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 GLN B 110 GLN B 172 ASN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN E 110 GLN F 394 ASN F 481 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.122721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.107596 restraints weight = 14825.221| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.39 r_work: 0.3191 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 10000 Z= 0.369 Angle : 0.757 8.696 13652 Z= 0.388 Chirality : 0.049 0.228 1498 Planarity : 0.005 0.056 1764 Dihedral : 8.111 74.716 1443 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.98 % Favored : 86.02 % Rotamer: Outliers : 6.02 % Allowed : 16.17 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.68 (0.22), residues: 1252 helix: -5.03 (0.23), residues: 56 sheet: -1.84 (0.25), residues: 432 loop : -2.71 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 509 TYR 0.020 0.002 TYR A 189 PHE 0.026 0.003 PHE C 377 TRP 0.025 0.003 TRP D 167 HIS 0.027 0.003 HIS B 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00831 / 0.37 ( 9982) covalent geometry : angle 0.75049 / 0.39 (13614) SS BOND : bond 0.00588 / 0.45 ( 16) SS BOND : angle 1.39391 / 0.88 ( 32) hydrogen bonds : bond 0.04419 / 2.90 ( 174) hydrogen bonds : angle 6.85681 / 4.55 ( 447) link_NAG-ASN : bond 0.01336 / 0.70 ( 2) link_NAG-ASN : angle 3.89566 / 2.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 222 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 12 VAL cc_start: 0.8632 (OUTLIER) cc_final: 0.8407 (p) REVERT: A 25 SER cc_start: 0.8426 (t) cc_final: 0.8102 (m) REVERT: A 55 SER cc_start: 0.8502 (m) cc_final: 0.7994 (t) REVERT: A 85 SER cc_start: 0.8481 (t) cc_final: 0.8095 (t) REVERT: A 154 LEU cc_start: 0.8777 (tp) cc_final: 0.8378 (tp) REVERT: A 182 VAL cc_start: 0.8096 (OUTLIER) cc_final: 0.7895 (m) REVERT: A 188 LEU cc_start: 0.7964 (mm) cc_final: 0.7626 (mt) REVERT: B 6 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7510 (mt0) REVERT: B 76 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7929 (mpp80) REVERT: B 108 LEU cc_start: 0.8476 (tp) cc_final: 0.8273 (tp) REVERT: B 130 ASN cc_start: 0.7432 (OUTLIER) cc_final: 0.7209 (p0) REVERT: C 346 ARG cc_start: 0.8770 (mtt-85) cc_final: 0.8315 (mtt180) REVERT: C 354 ASN cc_start: 0.8439 (t0) cc_final: 0.8175 (t0) REVERT: C 355 ARG cc_start: 0.8096 (ttt90) cc_final: 0.7785 (ttm170) REVERT: C 360 ASN cc_start: 0.8346 (m110) cc_final: 0.7974 (t0) REVERT: C 393 THR cc_start: 0.8757 (t) cc_final: 0.8450 (p) REVERT: C 481 ASN cc_start: 0.8542 (m-40) cc_final: 0.8034 (t0) REVERT: C 508 TYR cc_start: 0.8536 (m-80) cc_final: 0.8285 (m-80) REVERT: C 511 VAL cc_start: 0.8797 (OUTLIER) cc_final: 0.8474 (t) REVERT: C 518 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8306 (mp) REVERT: D 25 SER cc_start: 0.8766 (t) cc_final: 0.8372 (p) REVERT: D 80 TYR cc_start: 0.8594 (m-80) cc_final: 0.8293 (m-80) REVERT: D 100 HIS cc_start: 0.6752 (OUTLIER) cc_final: 0.6456 (m90) REVERT: D 126 SER cc_start: 0.8764 (m) cc_final: 0.8487 (p) REVERT: D 133 SER cc_start: 0.8362 (t) cc_final: 0.8037 (t) REVERT: D 139 PRO cc_start: 0.8264 (Cg_endo) cc_final: 0.8057 (Cg_exo) REVERT: D 158 TYR cc_start: 0.8109 (p90) cc_final: 0.7748 (p90) REVERT: D 189 TYR cc_start: 0.8683 (m-80) cc_final: 0.8392 (m-80) REVERT: E 51 SER cc_start: 0.8358 (m) cc_final: 0.8019 (p) REVERT: E 71 THR cc_start: 0.8468 (m) cc_final: 0.8034 (t) REVERT: E 78 GLU cc_start: 0.7957 (pm20) cc_final: 0.7718 (pm20) REVERT: E 81 ASP cc_start: 0.8423 (t70) cc_final: 0.7949 (t70) REVERT: E 119 LEU cc_start: 0.6891 (mm) cc_final: 0.6670 (tp) REVERT: E 147 THR cc_start: 0.8227 (m) cc_final: 0.7701 (p) REVERT: E 198 THR cc_start: 0.7943 (m) cc_final: 0.7647 (p) REVERT: F 354 ASN cc_start: 0.7914 (t0) cc_final: 0.7508 (t0) REVERT: F 375 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.7194 (m-80) REVERT: F 386 LYS cc_start: 0.8425 (mmtt) cc_final: 0.8056 (mmtt) outliers start: 64 outliers final: 38 residues processed: 264 average time/residue: 0.1045 time to fit residues: 38.1543 Evaluate side-chains 257 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 210 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 130 ASN Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 517 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 41 optimal weight: 0.9980 chunk 119 optimal weight: 0.0770 chunk 39 optimal weight: 0.4980 chunk 3 optimal weight: 0.2980 chunk 67 optimal weight: 0.0980 chunk 98 optimal weight: 0.9980 chunk 60 optimal weight: 0.2980 chunk 87 optimal weight: 0.0970 chunk 20 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 overall best weight: 0.1736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 172 ASN B 190 HIS D 74 ASN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 394 ASN F 450 ASN F 481 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.126380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.111198 restraints weight = 14808.504| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.39 r_work: 0.3251 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10000 Z= 0.128 Angle : 0.604 6.513 13652 Z= 0.309 Chirality : 0.044 0.190 1498 Planarity : 0.005 0.058 1764 Dihedral : 7.289 75.465 1439 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.66 % Favored : 88.34 % Rotamer: Outliers : 4.70 % Allowed : 18.89 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.40 (0.23), residues: 1252 helix: -4.99 (0.23), residues: 56 sheet: -1.54 (0.26), residues: 418 loop : -2.56 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 454 TYR 0.012 0.001 TYR B 179 PHE 0.022 0.001 PHE C 377 TRP 0.016 0.002 TRP A 167 HIS 0.005 0.001 HIS D 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 9982) covalent geometry : angle 0.59873 / 0.31 (13614) SS BOND : bond 0.00359 / 0.25 ( 16) SS BOND : angle 1.19288 / 0.94 ( 32) hydrogen bonds : bond 0.03495 / 2.27 ( 174) hydrogen bonds : angle 6.24410 / 4.17 ( 447) link_NAG-ASN : bond 0.00526 / 0.25 ( 2) link_NAG-ASN : angle 2.78794 / 1.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 221 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 12 VAL cc_start: 0.8507 (OUTLIER) cc_final: 0.8305 (p) REVERT: A 32 TYR cc_start: 0.8798 (m-80) cc_final: 0.8503 (m-80) REVERT: A 55 SER cc_start: 0.8322 (m) cc_final: 0.7786 (t) REVERT: A 85 SER cc_start: 0.8393 (t) cc_final: 0.8007 (t) REVERT: A 154 LEU cc_start: 0.8751 (tp) cc_final: 0.8367 (tp) REVERT: B 31 SER cc_start: 0.8602 (m) cc_final: 0.8205 (p) REVERT: B 76 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7912 (mpp80) REVERT: B 151 LYS cc_start: 0.7140 (ttmm) cc_final: 0.6840 (ttmm) REVERT: B 173 LYS cc_start: 0.7094 (mmtp) cc_final: 0.6824 (mmmm) REVERT: C 346 ARG cc_start: 0.8680 (mtt-85) cc_final: 0.8186 (mtt180) REVERT: C 354 ASN cc_start: 0.8458 (t0) cc_final: 0.8178 (t0) REVERT: C 355 ARG cc_start: 0.8079 (ttt90) cc_final: 0.7827 (ttm170) REVERT: C 357 ARG cc_start: 0.7986 (mtp-110) cc_final: 0.7756 (mtp-110) REVERT: C 360 ASN cc_start: 0.8294 (m110) cc_final: 0.7872 (t0) REVERT: C 393 THR cc_start: 0.8843 (t) cc_final: 0.8635 (p) REVERT: C 448 ASN cc_start: 0.7820 (p0) cc_final: 0.7455 (p0) REVERT: C 467 ASP cc_start: 0.7389 (p0) cc_final: 0.6932 (p0) REVERT: C 481 ASN cc_start: 0.8556 (m-40) cc_final: 0.8062 (t0) REVERT: C 511 VAL cc_start: 0.8762 (OUTLIER) cc_final: 0.8516 (t) REVERT: C 518 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8265 (mp) REVERT: D 25 SER cc_start: 0.8726 (t) cc_final: 0.8343 (p) REVERT: D 80 TYR cc_start: 0.8536 (m-80) cc_final: 0.8247 (m-80) REVERT: D 100 HIS cc_start: 0.6494 (OUTLIER) cc_final: 0.6286 (m90) REVERT: D 126 SER cc_start: 0.8714 (m) cc_final: 0.8393 (p) REVERT: D 137 LEU cc_start: 0.7380 (mt) cc_final: 0.7140 (mp) REVERT: D 158 TYR cc_start: 0.7881 (p90) cc_final: 0.7219 (p90) REVERT: E 51 SER cc_start: 0.8045 (m) cc_final: 0.7737 (p) REVERT: E 71 THR cc_start: 0.8343 (m) cc_final: 0.7898 (t) REVERT: E 81 ASP cc_start: 0.8374 (t70) cc_final: 0.8019 (t0) REVERT: E 147 THR cc_start: 0.8195 (m) cc_final: 0.7659 (p) REVERT: E 198 THR cc_start: 0.7616 (m) cc_final: 0.7298 (p) REVERT: F 350 VAL cc_start: 0.8168 (t) cc_final: 0.7930 (p) REVERT: F 386 LYS cc_start: 0.8434 (mmtt) cc_final: 0.8048 (mmtt) outliers start: 50 outliers final: 33 residues processed: 249 average time/residue: 0.1023 time to fit residues: 35.5351 Evaluate side-chains 242 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 517 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.121279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.106481 restraints weight = 14902.954| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.37 r_work: 0.3195 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 10000 Z= 0.330 Angle : 0.747 11.705 13652 Z= 0.381 Chirality : 0.048 0.211 1498 Planarity : 0.005 0.050 1764 Dihedral : 7.723 76.352 1435 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.66 % Favored : 86.34 % Rotamer: Outliers : 5.26 % Allowed : 19.45 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.38 (0.23), residues: 1252 helix: -4.97 (0.26), residues: 56 sheet: -1.48 (0.26), residues: 426 loop : -2.60 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 498 TYR 0.019 0.002 TYR A 189 PHE 0.019 0.002 PHE C 375 TRP 0.022 0.002 TRP F 436 HIS 0.017 0.002 HIS B 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00751 / 0.33 ( 9982) covalent geometry : angle 0.74128 / 0.38 (13614) SS BOND : bond 0.00609 / 0.44 ( 16) SS BOND : angle 1.42358 / 0.96 ( 32) hydrogen bonds : bond 0.04164 / 2.69 ( 174) hydrogen bonds : angle 6.52555 / 4.31 ( 447) link_NAG-ASN : bond 0.00415 / 0.22 ( 2) link_NAG-ASN : angle 3.54543 / 1.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 211 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 12 VAL cc_start: 0.8566 (OUTLIER) cc_final: 0.8350 (p) REVERT: A 25 SER cc_start: 0.8443 (t) cc_final: 0.8155 (m) REVERT: A 32 TYR cc_start: 0.8757 (m-80) cc_final: 0.8442 (m-80) REVERT: A 55 SER cc_start: 0.8486 (m) cc_final: 0.7976 (t) REVERT: A 85 SER cc_start: 0.8457 (t) cc_final: 0.8080 (t) REVERT: A 93 LEU cc_start: 0.8269 (mt) cc_final: 0.8064 (mp) REVERT: A 154 LEU cc_start: 0.8815 (tp) cc_final: 0.8438 (tp) REVERT: A 188 LEU cc_start: 0.8065 (mm) cc_final: 0.7704 (mt) REVERT: B 6 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7497 (mt0) REVERT: B 55 SER cc_start: 0.8177 (t) cc_final: 0.7820 (m) REVERT: B 76 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7973 (mpp80) REVERT: B 130 ASN cc_start: 0.7457 (OUTLIER) cc_final: 0.7242 (p0) REVERT: C 346 ARG cc_start: 0.8751 (mtt-85) cc_final: 0.8304 (mtt180) REVERT: C 354 ASN cc_start: 0.8449 (t0) cc_final: 0.8202 (t0) REVERT: C 355 ARG cc_start: 0.8116 (ttt90) cc_final: 0.7828 (ttm170) REVERT: C 360 ASN cc_start: 0.8339 (m110) cc_final: 0.7928 (t0) REVERT: C 467 ASP cc_start: 0.7352 (p0) cc_final: 0.6929 (p0) REVERT: C 481 ASN cc_start: 0.8552 (m-40) cc_final: 0.8143 (t0) REVERT: C 511 VAL cc_start: 0.8800 (OUTLIER) cc_final: 0.8519 (t) REVERT: C 518 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8305 (mp) REVERT: D 25 SER cc_start: 0.8786 (t) cc_final: 0.8410 (p) REVERT: D 80 TYR cc_start: 0.8559 (m-80) cc_final: 0.8292 (m-80) REVERT: D 100 HIS cc_start: 0.6942 (OUTLIER) cc_final: 0.6487 (m90) REVERT: D 120 THR cc_start: 0.8745 (t) cc_final: 0.8381 (p) REVERT: D 126 SER cc_start: 0.8791 (m) cc_final: 0.8533 (p) REVERT: D 133 SER cc_start: 0.8468 (t) cc_final: 0.8111 (t) REVERT: D 139 PRO cc_start: 0.8277 (Cg_endo) cc_final: 0.8074 (Cg_exo) REVERT: D 154 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8322 (tp) REVERT: D 158 TYR cc_start: 0.8118 (p90) cc_final: 0.7485 (p90) REVERT: E 51 SER cc_start: 0.8336 (m) cc_final: 0.8002 (p) REVERT: E 71 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8036 (t) REVERT: E 81 ASP cc_start: 0.8361 (t70) cc_final: 0.8024 (t0) REVERT: E 147 THR cc_start: 0.8228 (m) cc_final: 0.7717 (p) REVERT: E 198 THR cc_start: 0.7866 (m) cc_final: 0.7585 (p) REVERT: F 375 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.7237 (m-80) REVERT: F 386 LYS cc_start: 0.8486 (mmtt) cc_final: 0.8117 (mmtt) REVERT: F 438 SER cc_start: 0.8600 (m) cc_final: 0.8183 (p) outliers start: 56 outliers final: 36 residues processed: 248 average time/residue: 0.1001 time to fit residues: 34.6194 Evaluate side-chains 257 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 211 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 130 ASN Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 517 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 17 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 58 optimal weight: 0.0980 chunk 68 optimal weight: 0.8980 chunk 87 optimal weight: 0.1980 chunk 43 optimal weight: 0.5980 chunk 22 optimal weight: 0.3980 chunk 65 optimal weight: 0.3980 chunk 15 optimal weight: 0.0870 chunk 78 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 overall best weight: 0.2358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS D 74 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.124063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.109179 restraints weight = 14693.795| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.35 r_work: 0.3242 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10000 Z= 0.151 Angle : 0.636 10.161 13652 Z= 0.322 Chirality : 0.045 0.193 1498 Planarity : 0.005 0.049 1764 Dihedral : 7.243 76.703 1433 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.14 % Favored : 87.86 % Rotamer: Outliers : 4.32 % Allowed : 20.96 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.23), residues: 1252 helix: -4.96 (0.24), residues: 56 sheet: -1.38 (0.26), residues: 426 loop : -2.44 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 454 TYR 0.013 0.001 TYR A 189 PHE 0.020 0.001 PHE C 377 TRP 0.016 0.002 TRP A 167 HIS 0.006 0.001 HIS D 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 9982) covalent geometry : angle 0.63197 / 0.32 (13614) SS BOND : bond 0.00432 / 0.32 ( 16) SS BOND : angle 1.05396 / 0.72 ( 32) hydrogen bonds : bond 0.03493 / 2.25 ( 174) hydrogen bonds : angle 6.14163 / 4.07 ( 447) link_NAG-ASN : bond 0.00221 / 0.12 ( 2) link_NAG-ASN : angle 2.87044 / 1.52 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 214 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 12 VAL cc_start: 0.8512 (OUTLIER) cc_final: 0.8306 (p) REVERT: A 25 SER cc_start: 0.8373 (t) cc_final: 0.8134 (m) REVERT: A 32 TYR cc_start: 0.8765 (m-80) cc_final: 0.8505 (m-80) REVERT: A 55 SER cc_start: 0.8295 (m) cc_final: 0.7775 (t) REVERT: A 85 SER cc_start: 0.8405 (t) cc_final: 0.8040 (t) REVERT: A 154 LEU cc_start: 0.8756 (tp) cc_final: 0.8396 (tp) REVERT: A 188 LEU cc_start: 0.8042 (mm) cc_final: 0.7762 (mt) REVERT: B 6 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7386 (mt0) REVERT: B 76 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7975 (mpp80) REVERT: B 151 LYS cc_start: 0.7181 (ttmm) cc_final: 0.6838 (ttmm) REVERT: B 173 LYS cc_start: 0.7187 (mmtp) cc_final: 0.6920 (mmmm) REVERT: C 346 ARG cc_start: 0.8709 (mtt-85) cc_final: 0.8232 (mtt180) REVERT: C 350 VAL cc_start: 0.8491 (t) cc_final: 0.8149 (p) REVERT: C 354 ASN cc_start: 0.8458 (t0) cc_final: 0.8222 (t0) REVERT: C 355 ARG cc_start: 0.8058 (ttt90) cc_final: 0.7775 (ttm170) REVERT: C 360 ASN cc_start: 0.8282 (m110) cc_final: 0.7909 (t0) REVERT: C 393 THR cc_start: 0.8940 (t) cc_final: 0.8659 (p) REVERT: C 425 LEU cc_start: 0.8325 (mp) cc_final: 0.8065 (mt) REVERT: C 448 ASN cc_start: 0.7868 (p0) cc_final: 0.7541 (p0) REVERT: C 467 ASP cc_start: 0.7347 (p0) cc_final: 0.6817 (p0) REVERT: C 481 ASN cc_start: 0.8491 (m-40) cc_final: 0.8238 (t0) REVERT: C 511 VAL cc_start: 0.8795 (OUTLIER) cc_final: 0.8547 (t) REVERT: C 518 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8242 (mp) REVERT: D 25 SER cc_start: 0.8831 (t) cc_final: 0.8437 (p) REVERT: D 80 TYR cc_start: 0.8562 (m-80) cc_final: 0.8324 (m-80) REVERT: D 100 HIS cc_start: 0.6826 (OUTLIER) cc_final: 0.6446 (m90) REVERT: D 101 GLN cc_start: 0.6793 (OUTLIER) cc_final: 0.6566 (mp10) REVERT: D 126 SER cc_start: 0.8747 (m) cc_final: 0.8464 (p) REVERT: D 158 TYR cc_start: 0.8008 (p90) cc_final: 0.7433 (p90) REVERT: E 51 SER cc_start: 0.8099 (m) cc_final: 0.7787 (p) REVERT: E 71 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.7954 (t) REVERT: E 81 ASP cc_start: 0.8327 (t70) cc_final: 0.8098 (t0) REVERT: E 147 THR cc_start: 0.8246 (m) cc_final: 0.7752 (p) REVERT: E 198 THR cc_start: 0.7683 (m) cc_final: 0.7400 (p) REVERT: F 386 LYS cc_start: 0.8531 (mmtt) cc_final: 0.8199 (mmtt) REVERT: F 438 SER cc_start: 0.8625 (m) cc_final: 0.8218 (p) REVERT: F 498 ARG cc_start: 0.8510 (mtt180) cc_final: 0.8284 (mtt90) outliers start: 46 outliers final: 30 residues processed: 240 average time/residue: 0.1013 time to fit residues: 33.8944 Evaluate side-chains 248 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 210 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 517 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 78 optimal weight: 0.0670 chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 15 optimal weight: 0.1980 chunk 75 optimal weight: 0.2980 chunk 76 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 99 optimal weight: 0.0970 chunk 119 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 84 optimal weight: 0.1980 overall best weight: 0.1716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 74 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.126296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.111250 restraints weight = 14663.837| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.37 r_work: 0.3254 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10000 Z= 0.124 Angle : 0.610 9.367 13652 Z= 0.309 Chirality : 0.044 0.218 1498 Planarity : 0.005 0.045 1764 Dihedral : 6.770 77.487 1427 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.26 % Favored : 88.74 % Rotamer: Outliers : 4.42 % Allowed : 21.43 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.05 (0.23), residues: 1252 helix: -4.91 (0.24), residues: 56 sheet: -1.22 (0.27), residues: 414 loop : -2.36 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 454 TYR 0.013 0.001 TYR C 508 PHE 0.025 0.001 PHE C 377 TRP 0.017 0.001 TRP A 167 HIS 0.004 0.001 HIS D 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 ( 9982) covalent geometry : angle 0.60720 / 0.31 (13614) SS BOND : bond 0.00341 / 0.25 ( 16) SS BOND : angle 0.89511 / 0.60 ( 32) hydrogen bonds : bond 0.03317 / 2.11 ( 174) hydrogen bonds : angle 5.82426 / 3.89 ( 447) link_NAG-ASN : bond 0.00146 / 0.08 ( 2) link_NAG-ASN : angle 2.52991 / 1.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 201 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 25 SER cc_start: 0.8373 (t) cc_final: 0.8130 (m) REVERT: A 32 TYR cc_start: 0.8737 (m-80) cc_final: 0.8442 (m-80) REVERT: A 55 SER cc_start: 0.8173 (m) cc_final: 0.7636 (t) REVERT: A 85 SER cc_start: 0.8309 (t) cc_final: 0.7981 (t) REVERT: A 154 LEU cc_start: 0.8694 (tp) cc_final: 0.8308 (tt) REVERT: B 6 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7353 (mt0) REVERT: B 76 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7967 (mpp80) REVERT: B 130 ASN cc_start: 0.7116 (OUTLIER) cc_final: 0.6874 (p0) REVERT: B 151 LYS cc_start: 0.6830 (ttmm) cc_final: 0.6491 (ttmm) REVERT: C 346 ARG cc_start: 0.8687 (mtt-85) cc_final: 0.8206 (mtt180) REVERT: C 357 ARG cc_start: 0.7971 (mtp-110) cc_final: 0.7768 (mtp-110) REVERT: C 393 THR cc_start: 0.8946 (t) cc_final: 0.8651 (p) REVERT: C 425 LEU cc_start: 0.8318 (mp) cc_final: 0.8056 (mt) REVERT: C 445 VAL cc_start: 0.7961 (OUTLIER) cc_final: 0.7643 (p) REVERT: C 448 ASN cc_start: 0.7821 (p0) cc_final: 0.7500 (p0) REVERT: C 467 ASP cc_start: 0.7304 (p0) cc_final: 0.6889 (p0) REVERT: C 481 ASN cc_start: 0.8473 (m-40) cc_final: 0.8171 (t0) REVERT: C 490 PHE cc_start: 0.8171 (t80) cc_final: 0.7949 (t80) REVERT: C 511 VAL cc_start: 0.8786 (OUTLIER) cc_final: 0.8557 (t) REVERT: C 518 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8241 (mp) REVERT: D 25 SER cc_start: 0.8774 (t) cc_final: 0.8430 (p) REVERT: D 100 HIS cc_start: 0.6534 (OUTLIER) cc_final: 0.6329 (m90) REVERT: D 126 SER cc_start: 0.8727 (m) cc_final: 0.8449 (p) REVERT: D 133 SER cc_start: 0.8541 (t) cc_final: 0.8168 (t) REVERT: D 137 LEU cc_start: 0.7352 (mt) cc_final: 0.6909 (mp) REVERT: E 71 THR cc_start: 0.8305 (m) cc_final: 0.7884 (t) REVERT: E 147 THR cc_start: 0.8249 (m) cc_final: 0.7803 (p) REVERT: F 386 LYS cc_start: 0.8510 (mmtt) cc_final: 0.8170 (mmtt) REVERT: F 438 SER cc_start: 0.8649 (m) cc_final: 0.8265 (p) REVERT: F 517 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7119 (tm) outliers start: 47 outliers final: 31 residues processed: 231 average time/residue: 0.0991 time to fit residues: 32.0995 Evaluate side-chains 228 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 130 ASN Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 517 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 55 optimal weight: 0.1980 chunk 33 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 75 optimal weight: 0.2980 chunk 39 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 58 optimal weight: 0.0670 chunk 84 optimal weight: 0.0870 overall best weight: 0.2096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 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 = 0.3602 r_free = 0.3602 target = 0.125881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.110835 restraints weight = 14669.022| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.37 r_work: 0.3263 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10000 Z= 0.136 Angle : 0.621 9.328 13652 Z= 0.314 Chirality : 0.044 0.229 1498 Planarity : 0.005 0.045 1764 Dihedral : 6.752 77.868 1427 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.42 % Favored : 88.58 % Rotamer: Outliers : 4.14 % Allowed : 21.52 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.23), residues: 1252 helix: -5.03 (0.25), residues: 44 sheet: -1.15 (0.27), residues: 406 loop : -2.28 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 454 TYR 0.014 0.001 TYR B 179 PHE 0.030 0.001 PHE C 377 TRP 0.014 0.001 TRP A 167 HIS 0.005 0.001 HIS D 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 9982) covalent geometry : angle 0.61818 / 0.31 (13614) SS BOND : bond 0.00346 / 0.26 ( 16) SS BOND : angle 0.85901 / 0.57 ( 32) hydrogen bonds : bond 0.03236 / 2.09 ( 174) hydrogen bonds : angle 5.79399 / 3.87 ( 447) link_NAG-ASN : bond 0.00153 / 0.08 ( 2) link_NAG-ASN : angle 2.46675 / 1.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 189 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 25 SER cc_start: 0.8344 (t) cc_final: 0.8112 (m) REVERT: A 32 TYR cc_start: 0.8736 (m-80) cc_final: 0.8473 (m-80) REVERT: A 85 SER cc_start: 0.8292 (t) cc_final: 0.7954 (t) REVERT: A 154 LEU cc_start: 0.8702 (tp) cc_final: 0.8356 (tp) REVERT: B 6 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7378 (mt0) REVERT: B 76 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7940 (mpp80) REVERT: B 130 ASN cc_start: 0.7078 (OUTLIER) cc_final: 0.6823 (p0) REVERT: B 151 LYS cc_start: 0.6784 (ttmm) cc_final: 0.6442 (ttmm) REVERT: C 346 ARG cc_start: 0.8667 (mtt-85) cc_final: 0.8169 (mtt180) REVERT: C 360 ASN cc_start: 0.8351 (m110) cc_final: 0.7982 (t0) REVERT: C 448 ASN cc_start: 0.7865 (p0) cc_final: 0.7511 (p0) REVERT: C 467 ASP cc_start: 0.7276 (p0) cc_final: 0.6879 (p0) REVERT: C 481 ASN cc_start: 0.8470 (m-40) cc_final: 0.8227 (t0) REVERT: C 486 PHE cc_start: 0.8664 (m-10) cc_final: 0.8286 (m-80) REVERT: C 490 PHE cc_start: 0.8200 (t80) cc_final: 0.7971 (t80) REVERT: C 511 VAL cc_start: 0.8784 (OUTLIER) cc_final: 0.8547 (t) REVERT: D 25 SER cc_start: 0.8779 (t) cc_final: 0.8436 (p) REVERT: D 126 SER cc_start: 0.8731 (m) cc_final: 0.8450 (p) REVERT: D 133 SER cc_start: 0.8542 (t) cc_final: 0.8178 (t) REVERT: D 137 LEU cc_start: 0.7376 (mt) cc_final: 0.6900 (mp) REVERT: D 178 THR cc_start: 0.8855 (m) cc_final: 0.8424 (p) REVERT: E 71 THR cc_start: 0.8313 (m) cc_final: 0.7883 (t) REVERT: E 147 THR cc_start: 0.8265 (m) cc_final: 0.7800 (p) REVERT: E 178 SER cc_start: 0.8613 (t) cc_final: 0.8397 (t) REVERT: E 198 THR cc_start: 0.7602 (m) cc_final: 0.7353 (p) REVERT: F 386 LYS cc_start: 0.8563 (mmtt) cc_final: 0.8224 (mmtt) REVERT: F 438 SER cc_start: 0.8651 (m) cc_final: 0.8276 (p) outliers start: 44 outliers final: 34 residues processed: 215 average time/residue: 0.1016 time to fit residues: 30.6927 Evaluate side-chains 227 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 130 ASN Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 517 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 109 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 105 optimal weight: 0.0870 chunk 30 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 116 optimal weight: 0.0870 chunk 47 optimal weight: 0.1980 chunk 22 optimal weight: 0.0770 overall best weight: 0.2294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 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 = 0.3609 r_free = 0.3609 target = 0.126487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.111324 restraints weight = 14525.935| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.41 r_work: 0.3275 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10000 Z= 0.144 Angle : 0.631 9.360 13652 Z= 0.319 Chirality : 0.045 0.246 1498 Planarity : 0.005 0.044 1764 Dihedral : 6.764 78.247 1427 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 4.42 % Allowed : 20.96 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.23), residues: 1252 helix: -5.02 (0.25), residues: 44 sheet: -1.08 (0.27), residues: 406 loop : -2.21 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 454 TYR 0.015 0.001 TYR C 508 PHE 0.032 0.001 PHE C 377 TRP 0.014 0.001 TRP A 167 HIS 0.006 0.001 HIS D 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 9982) covalent geometry : angle 0.62828 / 0.32 (13614) SS BOND : bond 0.00376 / 0.28 ( 16) SS BOND : angle 0.89826 / 0.60 ( 32) hydrogen bonds : bond 0.03236 / 2.08 ( 174) hydrogen bonds : angle 5.78866 / 3.87 ( 447) link_NAG-ASN : bond 0.00154 / 0.08 ( 2) link_NAG-ASN : angle 2.41272 / 1.26 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 199 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 25 SER cc_start: 0.8359 (t) cc_final: 0.8159 (m) REVERT: A 32 TYR cc_start: 0.8751 (m-80) cc_final: 0.8474 (m-80) REVERT: A 85 SER cc_start: 0.8288 (t) cc_final: 0.7946 (t) REVERT: A 154 LEU cc_start: 0.8715 (tp) cc_final: 0.8353 (tp) REVERT: B 6 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7525 (mt0) REVERT: B 46 VAL cc_start: 0.8223 (OUTLIER) cc_final: 0.8021 (m) REVERT: B 76 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7879 (mpp80) REVERT: B 151 LYS cc_start: 0.6769 (ttmm) cc_final: 0.6553 (ttmm) REVERT: B 194 SER cc_start: 0.5716 (OUTLIER) cc_final: 0.5347 (p) REVERT: C 346 ARG cc_start: 0.8628 (mtt-85) cc_final: 0.8133 (mtt180) REVERT: C 360 ASN cc_start: 0.8350 (m110) cc_final: 0.8069 (m110) REVERT: C 425 LEU cc_start: 0.8499 (mt) cc_final: 0.8271 (mt) REVERT: C 448 ASN cc_start: 0.7790 (p0) cc_final: 0.7462 (p0) REVERT: C 467 ASP cc_start: 0.7296 (p0) cc_final: 0.6896 (p0) REVERT: C 481 ASN cc_start: 0.8458 (m-40) cc_final: 0.8183 (t160) REVERT: C 486 PHE cc_start: 0.8679 (m-10) cc_final: 0.8310 (m-80) REVERT: C 494 SER cc_start: 0.8272 (m) cc_final: 0.8070 (p) REVERT: C 511 VAL cc_start: 0.8788 (OUTLIER) cc_final: 0.8552 (t) REVERT: C 518 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8318 (mp) REVERT: D 25 SER cc_start: 0.8797 (t) cc_final: 0.8465 (p) REVERT: D 126 SER cc_start: 0.8752 (m) cc_final: 0.8478 (p) REVERT: D 133 SER cc_start: 0.8585 (t) cc_final: 0.8226 (t) REVERT: D 137 LEU cc_start: 0.7438 (mt) cc_final: 0.6958 (mp) REVERT: D 163 VAL cc_start: 0.7231 (t) cc_final: 0.6953 (p) REVERT: D 178 THR cc_start: 0.8847 (m) cc_final: 0.8418 (p) REVERT: E 71 THR cc_start: 0.8352 (m) cc_final: 0.7937 (t) REVERT: E 78 GLU cc_start: 0.7490 (pm20) cc_final: 0.7241 (pm20) REVERT: E 147 THR cc_start: 0.8220 (m) cc_final: 0.7782 (p) REVERT: E 178 SER cc_start: 0.8608 (t) cc_final: 0.8400 (t) REVERT: E 198 THR cc_start: 0.7626 (m) cc_final: 0.7377 (p) REVERT: F 386 LYS cc_start: 0.8560 (mmtt) cc_final: 0.8235 (mmtt) REVERT: F 438 SER cc_start: 0.8636 (m) cc_final: 0.8274 (p) outliers start: 47 outliers final: 36 residues processed: 229 average time/residue: 0.1048 time to fit residues: 33.3483 Evaluate side-chains 240 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 198 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 151 LYS Chi-restraints excluded: chain F residue 375 PHE Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 462 LYS Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 514 SER Chi-restraints excluded: chain F residue 517 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 65 optimal weight: 0.0870 chunk 24 optimal weight: 0.4980 chunk 98 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 50 optimal weight: 0.4980 chunk 88 optimal weight: 0.0870 chunk 19 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 46 optimal weight: 0.1980 chunk 7 optimal weight: 0.8980 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 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 = 0.3605 r_free = 0.3605 target = 0.126111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.110799 restraints weight = 14719.785| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.43 r_work: 0.3270 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10000 Z= 0.153 Angle : 0.640 9.392 13652 Z= 0.322 Chirality : 0.045 0.249 1498 Planarity : 0.005 0.044 1764 Dihedral : 6.774 78.306 1427 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.74 % Favored : 88.26 % Rotamer: Outliers : 4.04 % Allowed : 21.52 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.23), residues: 1252 helix: -4.99 (0.26), residues: 44 sheet: -1.13 (0.26), residues: 442 loop : -2.20 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 454 TYR 0.015 0.001 TYR C 508 PHE 0.032 0.002 PHE C 377 TRP 0.014 0.002 TRP A 167 HIS 0.007 0.001 HIS D 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 9982) covalent geometry : angle 0.63723 / 0.32 (13614) SS BOND : bond 0.00361 / 0.27 ( 16) SS BOND : angle 0.89760 / 0.60 ( 32) hydrogen bonds : bond 0.03269 / 2.11 ( 174) hydrogen bonds : angle 5.82938 / 3.90 ( 447) link_NAG-ASN : bond 0.00180 / 0.09 ( 2) link_NAG-ASN : angle 2.41361 / 1.26 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2731.68 seconds wall clock time: 47 minutes 44.56 seconds (2864.56 seconds total)