Starting phenix.real_space_refine on Wed Mar 4 01:11:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wk0_32554/03_2026/7wk0_32554.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wk0_32554/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7wk0_32554/03_2026/7wk0_32554.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wk0_32554/03_2026/7wk0_32554.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wk0_32554/03_2026/7wk0_32554.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wk0_32554/03_2026/7wk0_32554.map" } 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-5986/lib/python3.9/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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.37, 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: 0.72 Conformation dependent library (CDL) restraints added in 477.9 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: 0.32 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: 1.36 Time building geometry restraints manager: 0.99 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: 5574 17.71 - 35.42: 306 35.42 - 53.14: 45 53.14 - 70.85: 18 70.85 - 88.56: 1 Dihedral angle restraints: 5944 sinusoidal: 2288 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 5941 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: 10.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.230 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 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 : 11.091 88.559 3568 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 covalent geometry : bond 0.00428 ( 9982) covalent geometry : angle 0.65482 (13614) SS BOND : bond 0.00214 ( 16) SS BOND : angle 0.46490 ( 32) hydrogen bonds : bond 0.28683 ( 174) hydrogen bonds : angle 11.39510 ( 447) link_NAG-ASN : bond 0.00447 ( 2) link_NAG-ASN : angle 5.34599 ( 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 : 0.353 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: 0.1079 time to fit residues: 43.6707 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 : 0.320 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3670 r_free = 0.3670 target = 0.130510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.115398 restraints weight = 14752.144| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.38 r_work: 0.3349 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1598 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= 0.146 Angle : 0.612 6.554 13652 Z= 0.314 Chirality : 0.045 0.217 1498 Planarity : 0.005 0.044 1764 Dihedral : 8.074 71.790 1517 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.26 % Favored : 88.74 % Rotamer: Outliers : 5.83 % Allowed : 13.16 % 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 covalent geometry : bond 0.00330 ( 9982) covalent geometry : angle 0.60459 (13614) SS BOND : bond 0.00476 ( 16) SS BOND : angle 1.12032 ( 32) hydrogen bonds : bond 0.04401 ( 174) hydrogen bonds : angle 7.54228 ( 447) link_NAG-ASN : bond 0.00365 ( 2) link_NAG-ASN : angle 3.87188 ( 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 283 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 221 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 SER cc_start: 0.8140 (m) cc_final: 0.7835 (p) REVERT: A 55 SER cc_start: 0.8241 (m) cc_final: 0.7814 (t) REVERT: A 154 LEU cc_start: 0.8723 (tp) cc_final: 0.8373 (tp) REVERT: B 151 LYS cc_start: 0.7308 (ttmm) cc_final: 0.7037 (ttmm) REVERT: C 346 ARG cc_start: 0.8704 (mtt-85) cc_final: 0.8429 (mtt90) REVERT: C 354 ASN cc_start: 0.8469 (t0) cc_final: 0.8191 (t0) REVERT: C 355 ARG cc_start: 0.8088 (ttt90) cc_final: 0.7779 (ttm170) REVERT: C 360 ASN cc_start: 0.8245 (m110) cc_final: 0.7903 (t0) REVERT: C 454 ARG cc_start: 0.8398 (ttm-80) cc_final: 0.8131 (ttm-80) REVERT: C 467 ASP cc_start: 0.7533 (p0) cc_final: 0.6901 (p0) REVERT: C 481 ASN cc_start: 0.8411 (m-40) cc_final: 0.8167 (m110) REVERT: C 508 TYR cc_start: 0.8645 (m-80) cc_final: 0.8393 (m-80) REVERT: D 25 SER cc_start: 0.8763 (t) cc_final: 0.8426 (p) REVERT: D 37 VAL cc_start: 0.8456 (OUTLIER) cc_final: 0.8183 (m) REVERT: D 126 SER cc_start: 0.8628 (m) cc_final: 0.8348 (p) REVERT: D 134 VAL cc_start: 0.8885 (t) cc_final: 0.8664 (m) REVERT: E 77 VAL cc_start: 0.7531 (OUTLIER) cc_final: 0.7306 (m) REVERT: E 78 GLU cc_start: 0.7814 (pm20) cc_final: 0.7228 (pm20) REVERT: E 81 ASP cc_start: 0.8490 (t70) cc_final: 0.8162 (t70) REVERT: E 119 LEU cc_start: 0.6809 (mm) cc_final: 0.6604 (tp) REVERT: E 147 THR cc_start: 0.8292 (m) cc_final: 0.7812 (p) REVERT: F 357 ARG cc_start: 0.8020 (mtp-110) cc_final: 0.7624 (mtp-110) REVERT: F 362 VAL cc_start: 0.8554 (t) cc_final: 0.8232 (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: 0.7350 (m110) REVERT: F 403 ARG cc_start: 0.7389 (mtm-85) cc_final: 0.7059 (mtm-85) REVERT: F 503 VAL cc_start: 0.8888 (p) cc_final: 0.8657 (t) REVERT: F 517 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7334 (tp) outliers start: 62 outliers final: 38 residues processed: 267 average time/residue: 0.1088 time to fit residues: 39.3432 Evaluate side-chains 241 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 200 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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: 0.0970 chunk 120 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 116 optimal weight: 0.0980 chunk 86 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 99 optimal weight: 0.0170 chunk 91 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 64 optimal weight: 0.3980 chunk 24 optimal weight: 0.0980 overall best weight: 0.1416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3653 r_free = 0.3653 target = 0.129493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.114264 restraints weight = 14961.014| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.38 r_work: 0.3333 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1946 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= 0.114 Angle : 0.578 7.513 13652 Z= 0.294 Chirality : 0.044 0.211 1498 Planarity : 0.004 0.040 1764 Dihedral : 7.433 73.155 1488 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.10 % Favored : 88.90 % Rotamer: Outliers : 5.55 % Allowed : 15.79 % Favored : 78.67 % 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: -3.78 (0.22), residues: 1252 helix: -5.02 (0.25), residues: 56 sheet: -1.78 (0.26), residues: 394 loop : -2.85 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 346 TYR 0.011 0.001 TYR D 95 PHE 0.021 0.001 PHE C 377 TRP 0.012 0.001 TRP F 436 HIS 0.011 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9982) covalent geometry : angle 0.57315 (13614) SS BOND : bond 0.00350 ( 16) SS BOND : angle 0.82468 ( 32) hydrogen bonds : bond 0.03702 ( 174) hydrogen bonds : angle 6.86106 ( 447) link_NAG-ASN : bond 0.00303 ( 2) link_NAG-ASN : angle 3.51816 ( 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: 59 poor density : 195 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 17 SER cc_start: 0.8038 (m) cc_final: 0.7790 (p) REVERT: A 32 TYR cc_start: 0.8740 (m-80) cc_final: 0.8449 (m-80) REVERT: A 55 SER cc_start: 0.8208 (m) cc_final: 0.7758 (t) REVERT: A 85 SER cc_start: 0.8526 (t) cc_final: 0.8189 (t) REVERT: A 154 LEU cc_start: 0.8669 (tp) cc_final: 0.8321 (tp) REVERT: B 6 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7157 (mt0) REVERT: B 14 PRO cc_start: 0.8420 (Cg_endo) cc_final: 0.8120 (Cg_exo) REVERT: B 55 SER cc_start: 0.7991 (t) cc_final: 0.7610 (m) REVERT: B 76 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7927 (mpp80) REVERT: B 151 LYS cc_start: 0.7225 (ttmm) cc_final: 0.7014 (ttmm) REVERT: C 346 ARG cc_start: 0.8664 (mtt-85) cc_final: 0.8423 (mtt90) REVERT: C 355 ARG cc_start: 0.8084 (ttt90) cc_final: 0.7793 (ttm170) REVERT: C 360 ASN cc_start: 0.8273 (m110) cc_final: 0.7899 (t0) REVERT: C 448 ASN cc_start: 0.7751 (p0) cc_final: 0.7392 (p0) REVERT: C 454 ARG cc_start: 0.8390 (ttm-80) cc_final: 0.8138 (ttm-80) REVERT: C 467 ASP cc_start: 0.7480 (p0) cc_final: 0.6858 (p0) REVERT: C 481 ASN cc_start: 0.8478 (m-40) cc_final: 0.8211 (m110) REVERT: C 488 CYS cc_start: 0.7277 (m) cc_final: 0.6831 (m) REVERT: C 509 ARG cc_start: 0.8850 (mtt-85) cc_final: 0.8539 (mtt180) REVERT: C 511 VAL cc_start: 0.8730 (OUTLIER) cc_final: 0.8414 (t) REVERT: D 25 SER cc_start: 0.8720 (t) cc_final: 0.8351 (p) REVERT: D 37 VAL cc_start: 0.8357 (OUTLIER) cc_final: 0.8114 (m) REVERT: D 93 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7757 (tt) REVERT: D 126 SER cc_start: 0.8611 (m) cc_final: 0.8319 (p) REVERT: D 134 VAL cc_start: 0.8852 (t) cc_final: 0.8650 (m) REVERT: E 71 THR cc_start: 0.8276 (m) cc_final: 0.7893 (t) REVERT: E 77 VAL cc_start: 0.7449 (OUTLIER) cc_final: 0.7229 (m) REVERT: E 78 GLU cc_start: 0.7815 (pm20) cc_final: 0.7244 (pm20) REVERT: E 81 ASP cc_start: 0.8454 (t70) cc_final: 0.8146 (t70) REVERT: F 350 VAL cc_start: 0.8349 (t) cc_final: 0.8111 (p) REVERT: F 354 ASN cc_start: 0.8056 (t0) cc_final: 0.7721 (t0) REVERT: F 362 VAL cc_start: 0.8525 (t) cc_final: 0.8217 (p) REVERT: F 386 LYS cc_start: 0.8383 (mmtt) cc_final: 0.8082 (mmtt) REVERT: F 394 ASN cc_start: 0.7801 (m110) cc_final: 0.7587 (m110) REVERT: F 439 ASN cc_start: 0.8442 (t0) cc_final: 0.8145 (t0) REVERT: F 503 VAL cc_start: 0.8886 (p) cc_final: 0.8666 (t) REVERT: F 517 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7332 (tp) outliers start: 59 outliers final: 40 residues processed: 237 average time/residue: 0.1045 time to fit residues: 33.8621 Evaluate side-chains 239 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 192 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 52 THR Chi-restraints excluded: chain A residue 89 GLU 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 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 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 200 GLU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 350 VAL 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: 0.9980 chunk 22 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 67 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 481 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.119830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.104128 restraints weight = 15097.972| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.62 r_work: 0.3161 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.080 10000 Z= 0.385 Angle : 0.769 8.806 13652 Z= 0.393 Chirality : 0.050 0.232 1498 Planarity : 0.005 0.056 1764 Dihedral : 8.297 74.804 1485 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.74 % Favored : 86.26 % Rotamer: Outliers : 6.30 % Allowed : 15.98 % Favored : 77.73 % 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: -3.70 (0.22), residues: 1252 helix: -5.05 (0.22), residues: 56 sheet: -1.83 (0.25), residues: 436 loop : -2.74 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 67 TYR 0.021 0.002 TYR A 189 PHE 0.029 0.003 PHE C 377 TRP 0.027 0.003 TRP D 167 HIS 0.009 0.002 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00869 ( 9982) covalent geometry : angle 0.76173 (13614) SS BOND : bond 0.00583 ( 16) SS BOND : angle 1.41158 ( 32) hydrogen bonds : bond 0.04386 ( 174) hydrogen bonds : angle 6.83075 ( 447) link_NAG-ASN : bond 0.00984 ( 2) link_NAG-ASN : angle 4.08415 ( 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 288 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 221 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 12 VAL cc_start: 0.8632 (OUTLIER) cc_final: 0.8413 (p) REVERT: A 25 SER cc_start: 0.8477 (t) cc_final: 0.8156 (m) REVERT: A 55 SER cc_start: 0.8544 (m) cc_final: 0.8053 (t) REVERT: A 85 SER cc_start: 0.8484 (t) cc_final: 0.8095 (t) REVERT: A 154 LEU cc_start: 0.8793 (tp) cc_final: 0.8382 (tp) REVERT: A 182 VAL cc_start: 0.8163 (OUTLIER) cc_final: 0.7958 (m) REVERT: A 188 LEU cc_start: 0.8012 (mm) cc_final: 0.7679 (mt) REVERT: B 6 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7568 (mt0) REVERT: B 53 ARG cc_start: 0.8554 (ptp90) cc_final: 0.8147 (ptp90) REVERT: B 55 SER cc_start: 0.8178 (t) cc_final: 0.7819 (m) REVERT: B 76 ARG cc_start: 0.8213 (tpp80) cc_final: 0.7969 (mpp80) REVERT: B 108 LEU cc_start: 0.8509 (tp) cc_final: 0.8301 (tp) REVERT: B 130 ASN cc_start: 0.7456 (OUTLIER) cc_final: 0.7254 (p0) REVERT: C 346 ARG cc_start: 0.8781 (mtt-85) cc_final: 0.8328 (mtt180) REVERT: C 354 ASN cc_start: 0.8456 (t0) cc_final: 0.8242 (t0) REVERT: C 355 ARG cc_start: 0.8122 (ttt90) cc_final: 0.7903 (ttm170) REVERT: C 360 ASN cc_start: 0.8363 (m110) cc_final: 0.7991 (t0) REVERT: C 481 ASN cc_start: 0.8561 (m-40) cc_final: 0.8057 (t0) REVERT: C 518 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8300 (mp) REVERT: D 25 SER cc_start: 0.8797 (t) cc_final: 0.8420 (p) REVERT: D 80 TYR cc_start: 0.8626 (m-80) cc_final: 0.8354 (m-80) REVERT: D 100 HIS cc_start: 0.6837 (OUTLIER) cc_final: 0.6395 (m90) REVERT: D 126 SER cc_start: 0.8778 (m) cc_final: 0.8518 (p) REVERT: D 133 SER cc_start: 0.8419 (t) cc_final: 0.8087 (t) REVERT: D 139 PRO cc_start: 0.8296 (Cg_endo) cc_final: 0.8082 (Cg_exo) REVERT: D 158 TYR cc_start: 0.8144 (p90) cc_final: 0.7793 (p90) REVERT: D 189 TYR cc_start: 0.8717 (m-80) cc_final: 0.8419 (m-80) REVERT: E 51 SER cc_start: 0.8386 (m) cc_final: 0.8051 (p) REVERT: E 71 THR cc_start: 0.8492 (OUTLIER) cc_final: 0.8066 (t) REVERT: E 78 GLU cc_start: 0.8007 (pm20) cc_final: 0.7781 (pm20) REVERT: E 81 ASP cc_start: 0.8438 (t70) cc_final: 0.7958 (t0) REVERT: E 119 LEU cc_start: 0.6936 (mm) cc_final: 0.6698 (tp) REVERT: E 147 THR cc_start: 0.8260 (m) cc_final: 0.7745 (p) REVERT: E 198 THR cc_start: 0.7970 (m) cc_final: 0.7669 (p) REVERT: F 375 PHE cc_start: 0.7694 (OUTLIER) cc_final: 0.7225 (m-80) REVERT: F 386 LYS cc_start: 0.8443 (mmtt) cc_final: 0.8077 (mmtt) outliers start: 67 outliers final: 40 residues processed: 266 average time/residue: 0.1048 time to fit residues: 38.3142 Evaluate side-chains 261 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 213 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 177 HIS 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 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 43 LYS 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 71 THR 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 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: 1.9990 chunk 39 optimal weight: 0.1980 chunk 3 optimal weight: 0.2980 chunk 67 optimal weight: 0.1980 chunk 98 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 87 optimal weight: 0.0870 chunk 20 optimal weight: 3.9990 chunk 22 optimal weight: 0.2980 chunk 62 optimal weight: 0.7980 overall best weight: 0.2158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 ASN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 394 ASN 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 = 0.124355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.109008 restraints weight = 14894.326| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.47 r_work: 0.3255 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2840 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= 0.141 Angle : 0.624 7.108 13652 Z= 0.318 Chirality : 0.045 0.184 1498 Planarity : 0.005 0.057 1764 Dihedral : 7.573 75.641 1481 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.06 % Favored : 87.94 % Rotamer: Outliers : 4.98 % Allowed : 18.52 % Favored : 76.50 % 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: -5.07 (0.18), residues: 56 sheet: -1.48 (0.26), residues: 414 loop : -2.57 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 454 TYR 0.012 0.001 TYR D 111 PHE 0.024 0.001 PHE C 377 TRP 0.014 0.002 TRP A 167 HIS 0.005 0.001 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9982) covalent geometry : angle 0.61896 (13614) SS BOND : bond 0.00394 ( 16) SS BOND : angle 1.19164 ( 32) hydrogen bonds : bond 0.03572 ( 174) hydrogen bonds : angle 6.34335 ( 447) link_NAG-ASN : bond 0.00411 ( 2) link_NAG-ASN : angle 3.05934 ( 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 276 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 223 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 17 SER cc_start: 0.8091 (m) cc_final: 0.7852 (p) REVERT: A 32 TYR cc_start: 0.8765 (m-80) cc_final: 0.8491 (m-80) REVERT: A 55 SER cc_start: 0.8306 (m) cc_final: 0.7815 (t) REVERT: A 85 SER cc_start: 0.8467 (t) cc_final: 0.8085 (t) REVERT: A 154 LEU cc_start: 0.8793 (tp) cc_final: 0.8386 (tp) REVERT: B 55 SER cc_start: 0.8164 (t) cc_final: 0.7799 (m) REVERT: B 76 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7995 (mpp80) REVERT: B 173 LYS cc_start: 0.7247 (mmtp) cc_final: 0.6972 (mmmm) REVERT: C 346 ARG cc_start: 0.8674 (mtt-85) cc_final: 0.8191 (mtt180) REVERT: C 354 ASN cc_start: 0.8449 (t0) cc_final: 0.8204 (t0) REVERT: C 360 ASN cc_start: 0.8302 (m110) cc_final: 0.7922 (t0) REVERT: C 448 ASN cc_start: 0.7869 (p0) cc_final: 0.7530 (p0) REVERT: C 467 ASP cc_start: 0.7404 (p0) cc_final: 0.6981 (p0) REVERT: C 481 ASN cc_start: 0.8565 (m-40) cc_final: 0.8094 (t0) REVERT: C 489 TYR cc_start: 0.8659 (m-80) cc_final: 0.8323 (m-80) REVERT: C 511 VAL cc_start: 0.8773 (OUTLIER) cc_final: 0.8500 (t) REVERT: C 518 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8273 (mp) REVERT: D 4 LEU cc_start: 0.8692 (mt) cc_final: 0.8482 (mt) REVERT: D 25 SER cc_start: 0.8763 (t) cc_final: 0.8409 (p) REVERT: D 45 LEU cc_start: 0.8433 (mp) cc_final: 0.8220 (mt) REVERT: D 80 TYR cc_start: 0.8561 (m-80) cc_final: 0.8313 (m-80) REVERT: D 100 HIS cc_start: 0.6580 (OUTLIER) cc_final: 0.6376 (m90) REVERT: D 126 SER cc_start: 0.8741 (m) cc_final: 0.8428 (p) REVERT: D 133 SER cc_start: 0.8409 (t) cc_final: 0.8094 (t) REVERT: D 137 LEU cc_start: 0.7386 (mt) cc_final: 0.7174 (mp) REVERT: D 158 TYR cc_start: 0.7937 (p90) cc_final: 0.7615 (p90) REVERT: E 51 SER cc_start: 0.8137 (m) cc_final: 0.7819 (p) REVERT: E 81 ASP cc_start: 0.8350 (t70) cc_final: 0.8000 (t0) REVERT: E 147 THR cc_start: 0.8255 (m) cc_final: 0.7772 (p) REVERT: F 350 VAL cc_start: 0.8309 (t) cc_final: 0.8046 (p) REVERT: F 386 LYS cc_start: 0.8469 (mmtt) cc_final: 0.8120 (mmtt) outliers start: 53 outliers final: 35 residues processed: 252 average time/residue: 0.0988 time to fit residues: 34.4015 Evaluate side-chains 245 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 206 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 177 HIS 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 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 154 SER 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 36 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 54 optimal weight: 0.2980 chunk 53 optimal weight: 0.2980 chunk 16 optimal weight: 0.2980 chunk 109 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 80 optimal weight: 0.0770 chunk 49 optimal weight: 0.3980 chunk 74 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 overall best weight: 0.2738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** 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 = 0.3592 r_free = 0.3592 target = 0.125456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.110424 restraints weight = 14798.786| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.38 r_work: 0.3263 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10000 Z= 0.161 Angle : 0.633 9.481 13652 Z= 0.321 Chirality : 0.045 0.201 1498 Planarity : 0.005 0.050 1764 Dihedral : 7.297 76.791 1477 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.22 % Favored : 87.78 % Rotamer: Outliers : 5.45 % Allowed : 19.17 % Favored : 75.38 % 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: -3.25 (0.23), residues: 1252 helix: -5.02 (0.20), residues: 56 sheet: -1.33 (0.27), residues: 398 loop : -2.51 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 454 TYR 0.014 0.001 TYR C 508 PHE 0.014 0.001 PHE C 375 TRP 0.014 0.001 TRP F 436 HIS 0.006 0.001 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 9982) covalent geometry : angle 0.62889 (13614) SS BOND : bond 0.00411 ( 16) SS BOND : angle 1.00065 ( 32) hydrogen bonds : bond 0.03580 ( 174) hydrogen bonds : angle 6.15629 ( 447) link_NAG-ASN : bond 0.00259 ( 2) link_NAG-ASN : angle 3.15265 ( 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 261 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 203 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 17 SER cc_start: 0.8068 (m) cc_final: 0.7866 (p) REVERT: A 55 SER cc_start: 0.8263 (m) cc_final: 0.7771 (t) REVERT: A 85 SER cc_start: 0.8395 (t) cc_final: 0.8018 (t) REVERT: A 154 LEU cc_start: 0.8754 (tp) cc_final: 0.8374 (tp) REVERT: A 182 VAL cc_start: 0.8057 (OUTLIER) cc_final: 0.7748 (p) REVERT: B 6 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7374 (mt0) REVERT: B 55 SER cc_start: 0.8139 (t) cc_final: 0.7769 (m) REVERT: B 76 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7976 (mpp80) REVERT: B 130 ASN cc_start: 0.7220 (OUTLIER) cc_final: 0.7012 (p0) REVERT: B 173 LYS cc_start: 0.7243 (mmtp) cc_final: 0.6982 (mmmm) REVERT: C 346 ARG cc_start: 0.8702 (mtt-85) cc_final: 0.8235 (mtt180) REVERT: C 360 ASN cc_start: 0.8334 (m110) cc_final: 0.7960 (t0) REVERT: C 448 ASN cc_start: 0.7891 (p0) cc_final: 0.7543 (p0) REVERT: C 467 ASP cc_start: 0.7391 (p0) cc_final: 0.6745 (p0) REVERT: C 481 ASN cc_start: 0.8529 (m-40) cc_final: 0.8013 (t0) REVERT: C 489 TYR cc_start: 0.8556 (m-80) cc_final: 0.8134 (m-80) REVERT: C 490 PHE cc_start: 0.8247 (t80) cc_final: 0.8038 (t80) REVERT: C 511 VAL cc_start: 0.8809 (OUTLIER) cc_final: 0.8544 (t) REVERT: C 518 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8276 (mp) REVERT: D 25 SER cc_start: 0.8769 (t) cc_final: 0.8427 (p) REVERT: D 100 HIS cc_start: 0.6538 (OUTLIER) cc_final: 0.6235 (m90) REVERT: D 101 GLN cc_start: 0.6824 (OUTLIER) cc_final: 0.6595 (mp10) REVERT: D 126 SER cc_start: 0.8767 (m) cc_final: 0.8470 (p) REVERT: D 133 SER cc_start: 0.8522 (t) cc_final: 0.8154 (t) REVERT: E 51 SER cc_start: 0.8131 (m) cc_final: 0.7816 (p) REVERT: E 71 THR cc_start: 0.8377 (OUTLIER) cc_final: 0.7988 (t) REVERT: E 81 ASP cc_start: 0.8271 (t70) cc_final: 0.7974 (t0) REVERT: E 147 THR cc_start: 0.8277 (m) cc_final: 0.7801 (p) REVERT: F 354 ASN cc_start: 0.8027 (t0) cc_final: 0.7614 (t0) REVERT: F 386 LYS cc_start: 0.8431 (mmtt) cc_final: 0.8110 (mmtt) REVERT: F 438 SER cc_start: 0.8625 (m) cc_final: 0.8191 (p) outliers start: 58 outliers final: 40 residues processed: 240 average time/residue: 0.0988 time to fit residues: 32.3447 Evaluate side-chains 248 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 199 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 177 HIS 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 106 THR 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 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 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 196 THR 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 118 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 17 optimal weight: 0.9980 chunk 63 optimal weight: 0.4980 chunk 58 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 43 optimal weight: 0.0060 chunk 22 optimal weight: 0.6980 chunk 65 optimal weight: 0.2980 chunk 15 optimal weight: 0.0980 chunk 78 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN ** 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 = 0.3593 r_free = 0.3593 target = 0.125409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.110351 restraints weight = 14665.734| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.37 r_work: 0.3237 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10000 Z= 0.169 Angle : 0.633 9.662 13652 Z= 0.322 Chirality : 0.045 0.206 1498 Planarity : 0.005 0.046 1764 Dihedral : 7.289 77.240 1477 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.74 % Favored : 88.26 % Rotamer: Outliers : 5.73 % Allowed : 18.98 % 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: -3.13 (0.23), residues: 1252 helix: -4.99 (0.21), residues: 56 sheet: -1.24 (0.27), residues: 406 loop : -2.42 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 454 TYR 0.014 0.001 TYR C 508 PHE 0.017 0.001 PHE C 377 TRP 0.014 0.002 TRP F 436 HIS 0.006 0.001 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 9982) covalent geometry : angle 0.62891 (13614) SS BOND : bond 0.00395 ( 16) SS BOND : angle 0.98329 ( 32) hydrogen bonds : bond 0.03529 ( 174) hydrogen bonds : angle 6.02266 ( 447) link_NAG-ASN : bond 0.00215 ( 2) link_NAG-ASN : angle 2.90919 ( 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: 61 poor density : 199 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 17 SER cc_start: 0.8061 (m) cc_final: 0.7852 (p) REVERT: A 25 SER cc_start: 0.8390 (t) cc_final: 0.8159 (m) REVERT: A 32 TYR cc_start: 0.8740 (m-80) cc_final: 0.8450 (m-80) REVERT: A 85 SER cc_start: 0.8345 (t) cc_final: 0.7959 (t) REVERT: A 154 LEU cc_start: 0.8721 (tp) cc_final: 0.8335 (tp) REVERT: A 182 VAL cc_start: 0.8018 (OUTLIER) cc_final: 0.7710 (p) REVERT: B 6 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7364 (mt0) REVERT: B 31 SER cc_start: 0.8563 (m) cc_final: 0.8264 (p) REVERT: B 76 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7960 (mpp80) REVERT: B 173 LYS cc_start: 0.7141 (mmtp) cc_final: 0.6864 (mmmm) REVERT: C 346 ARG cc_start: 0.8676 (mtt-85) cc_final: 0.8181 (mtt180) REVERT: C 360 ASN cc_start: 0.8331 (m110) cc_final: 0.7939 (t0) REVERT: C 425 LEU cc_start: 0.8333 (mp) cc_final: 0.8075 (mt) REVERT: C 448 ASN cc_start: 0.7884 (p0) cc_final: 0.7503 (p0) REVERT: C 467 ASP cc_start: 0.7313 (p0) cc_final: 0.6903 (p0) REVERT: C 481 ASN cc_start: 0.8491 (m-40) cc_final: 0.8250 (t0) REVERT: C 511 VAL cc_start: 0.8798 (OUTLIER) cc_final: 0.8549 (t) REVERT: C 518 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8330 (mp) REVERT: D 25 SER cc_start: 0.8757 (t) cc_final: 0.8405 (p) REVERT: D 100 HIS cc_start: 0.6597 (OUTLIER) cc_final: 0.6271 (m90) REVERT: D 101 GLN cc_start: 0.6782 (OUTLIER) cc_final: 0.6559 (mp10) REVERT: D 126 SER cc_start: 0.8754 (m) cc_final: 0.8465 (p) REVERT: D 133 SER cc_start: 0.8434 (t) cc_final: 0.8071 (t) REVERT: E 51 SER cc_start: 0.8122 (m) cc_final: 0.7788 (p) REVERT: E 71 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.7959 (t) REVERT: E 81 ASP cc_start: 0.8213 (t70) cc_final: 0.7947 (t0) REVERT: E 147 THR cc_start: 0.8256 (m) cc_final: 0.7795 (p) REVERT: F 354 ASN cc_start: 0.7892 (t0) cc_final: 0.7539 (t0) REVERT: F 386 LYS cc_start: 0.8468 (mmtt) cc_final: 0.8128 (mmtt) REVERT: F 438 SER cc_start: 0.8624 (m) cc_final: 0.8208 (p) outliers start: 61 outliers final: 42 residues processed: 239 average time/residue: 0.1037 time to fit residues: 34.3037 Evaluate side-chains 248 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 198 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 177 HIS 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 76 ARG Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 154 SER 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 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 D residue 193 SER 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 71 THR Chi-restraints excluded: chain E residue 118 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 78 optimal weight: 0.0980 chunk 31 optimal weight: 0.9980 chunk 9 optimal weight: 0.2980 chunk 15 optimal weight: 0.0970 chunk 75 optimal weight: 0.2980 chunk 76 optimal weight: 0.9990 chunk 33 optimal weight: 0.0060 chunk 99 optimal weight: 0.2980 chunk 119 optimal weight: 0.9980 chunk 83 optimal weight: 0.1980 chunk 84 optimal weight: 0.0980 overall best weight: 0.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN ** 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 = 0.3637 r_free = 0.3637 target = 0.128588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.113143 restraints weight = 14686.764| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.45 r_work: 0.3299 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 10000 Z= 0.103 Angle : 0.587 9.443 13652 Z= 0.296 Chirality : 0.044 0.200 1498 Planarity : 0.004 0.045 1764 Dihedral : 6.792 78.060 1475 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.02 % Favored : 88.98 % Rotamer: Outliers : 4.42 % Allowed : 20.58 % Favored : 75.00 % 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: -3.01 (0.23), residues: 1252 helix: -4.90 (0.22), residues: 56 sheet: -1.12 (0.27), residues: 416 loop : -2.38 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 454 TYR 0.012 0.001 TYR C 508 PHE 0.014 0.001 PHE C 375 TRP 0.018 0.001 TRP A 167 HIS 0.003 0.001 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9982) covalent geometry : angle 0.58467 (13614) SS BOND : bond 0.00258 ( 16) SS BOND : angle 0.67494 ( 32) hydrogen bonds : bond 0.03062 ( 174) hydrogen bonds : angle 5.72857 ( 447) link_NAG-ASN : bond 0.00093 ( 2) link_NAG-ASN : angle 2.30025 ( 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 251 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 204 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 17 SER cc_start: 0.7951 (m) cc_final: 0.7739 (p) REVERT: A 25 SER cc_start: 0.8368 (t) cc_final: 0.8144 (m) REVERT: A 32 TYR cc_start: 0.8730 (m-80) cc_final: 0.8499 (m-80) REVERT: A 85 SER cc_start: 0.8297 (t) cc_final: 0.7920 (t) REVERT: A 154 LEU cc_start: 0.8594 (tp) cc_final: 0.8170 (tt) REVERT: B 6 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7581 (mt0) REVERT: B 76 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7920 (mpp80) REVERT: B 151 LYS cc_start: 0.6710 (ttmm) cc_final: 0.6421 (ttmm) REVERT: C 346 ARG cc_start: 0.8638 (mtt-85) cc_final: 0.8130 (mtt180) REVERT: C 425 LEU cc_start: 0.8277 (mp) cc_final: 0.8054 (mt) REVERT: C 448 ASN cc_start: 0.7770 (p0) cc_final: 0.7426 (p0) REVERT: C 467 ASP cc_start: 0.7353 (p0) cc_final: 0.6923 (p0) REVERT: C 481 ASN cc_start: 0.8472 (m-40) cc_final: 0.8175 (t160) REVERT: C 486 PHE cc_start: 0.8663 (m-10) cc_final: 0.8267 (m-80) REVERT: C 489 TYR cc_start: 0.8512 (m-80) cc_final: 0.8148 (m-80) REVERT: D 25 SER cc_start: 0.8716 (t) cc_final: 0.8380 (p) REVERT: D 37 VAL cc_start: 0.8286 (OUTLIER) cc_final: 0.8048 (m) REVERT: D 126 SER cc_start: 0.8724 (m) cc_final: 0.8423 (p) REVERT: D 133 SER cc_start: 0.8568 (t) cc_final: 0.8203 (t) REVERT: D 137 LEU cc_start: 0.7420 (mt) cc_final: 0.7156 (mp) REVERT: D 178 THR cc_start: 0.8872 (m) cc_final: 0.8436 (p) REVERT: E 71 THR cc_start: 0.8305 (m) cc_final: 0.7886 (t) REVERT: E 81 ASP cc_start: 0.8221 (t70) cc_final: 0.8012 (t0) REVERT: E 147 THR cc_start: 0.8219 (m) cc_final: 0.7801 (p) REVERT: F 386 LYS cc_start: 0.8514 (mmtt) cc_final: 0.8133 (mmtt) REVERT: F 438 SER cc_start: 0.8665 (m) cc_final: 0.8263 (p) REVERT: F 495 TYR cc_start: 0.7468 (m-10) cc_final: 0.6983 (m-10) REVERT: F 517 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7102 (tm) outliers start: 47 outliers final: 33 residues processed: 235 average time/residue: 0.1009 time to fit residues: 32.5080 Evaluate side-chains 237 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 200 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 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 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 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 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 102 ILE Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 118 THR 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 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: 0.0770 chunk 118 optimal weight: 0.6980 chunk 55 optimal weight: 0.0980 chunk 33 optimal weight: 0.0020 chunk 41 optimal weight: 0.5980 chunk 75 optimal weight: 0.2980 chunk 39 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 58 optimal weight: 0.0970 chunk 84 optimal weight: 0.1980 overall best weight: 0.0944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN ** B 172 ASN ** 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 = 0.3648 r_free = 0.3648 target = 0.129245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.113900 restraints weight = 14666.992| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.45 r_work: 0.3315 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10000 Z= 0.104 Angle : 0.597 9.296 13652 Z= 0.302 Chirality : 0.044 0.227 1498 Planarity : 0.005 0.044 1764 Dihedral : 6.616 78.448 1474 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer: Outliers : 3.85 % Allowed : 21.62 % Favored : 74.53 % 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: -2.86 (0.23), residues: 1252 helix: -4.84 (0.24), residues: 56 sheet: -0.99 (0.27), residues: 410 loop : -2.29 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 509 TYR 0.014 0.001 TYR A 189 PHE 0.015 0.001 PHE A 29 TRP 0.015 0.001 TRP A 167 HIS 0.004 0.001 HIS D 99 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9982) covalent geometry : angle 0.59533 (13614) SS BOND : bond 0.00283 ( 16) SS BOND : angle 0.61023 ( 32) hydrogen bonds : bond 0.03051 ( 174) hydrogen bonds : angle 5.65997 ( 447) link_NAG-ASN : bond 0.00093 ( 2) link_NAG-ASN : angle 2.21463 ( 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 248 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 207 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 SER cc_start: 0.8314 (t) cc_final: 0.8099 (m) REVERT: A 32 TYR cc_start: 0.8712 (m-80) cc_final: 0.8476 (m-80) REVERT: A 85 SER cc_start: 0.8265 (t) cc_final: 0.7879 (t) REVERT: A 154 LEU cc_start: 0.8530 (tp) cc_final: 0.8203 (tp) REVERT: B 6 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7456 (mt0) REVERT: B 76 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7885 (mpp80) REVERT: B 146 VAL cc_start: 0.8650 (t) cc_final: 0.8366 (p) REVERT: C 346 ARG cc_start: 0.8572 (mtt-85) cc_final: 0.8104 (mtt180) REVERT: C 360 ASN cc_start: 0.8352 (m110) cc_final: 0.8068 (m110) REVERT: C 448 ASN cc_start: 0.7599 (p0) cc_final: 0.7302 (p0) REVERT: C 467 ASP cc_start: 0.7359 (p0) cc_final: 0.7015 (p0) REVERT: C 481 ASN cc_start: 0.8459 (m-40) cc_final: 0.8164 (t160) REVERT: C 486 PHE cc_start: 0.8651 (m-10) cc_final: 0.8260 (m-80) REVERT: D 18 LEU cc_start: 0.8468 (pp) cc_final: 0.8233 (tt) REVERT: D 25 SER cc_start: 0.8684 (t) cc_final: 0.8335 (p) REVERT: D 37 VAL cc_start: 0.8286 (OUTLIER) cc_final: 0.8036 (m) REVERT: D 126 SER cc_start: 0.8717 (m) cc_final: 0.8435 (p) REVERT: D 133 SER cc_start: 0.8558 (t) cc_final: 0.8195 (t) REVERT: D 137 LEU cc_start: 0.7388 (mt) cc_final: 0.7106 (mp) REVERT: D 163 VAL cc_start: 0.7090 (t) cc_final: 0.6786 (p) REVERT: D 178 THR cc_start: 0.8853 (m) cc_final: 0.8429 (p) REVERT: E 71 THR cc_start: 0.8315 (m) cc_final: 0.7885 (t) REVERT: E 81 ASP cc_start: 0.8328 (t70) cc_final: 0.8113 (t0) REVERT: E 147 THR cc_start: 0.8224 (m) cc_final: 0.7833 (p) REVERT: F 386 LYS cc_start: 0.8545 (mmtt) cc_final: 0.8182 (mmtt) REVERT: F 438 SER cc_start: 0.8648 (m) cc_final: 0.8295 (p) REVERT: F 495 TYR cc_start: 0.7426 (m-10) cc_final: 0.6995 (m-10) outliers start: 41 outliers final: 37 residues processed: 232 average time/residue: 0.1084 time to fit residues: 34.5839 Evaluate side-chains 246 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 206 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 153 CYS Chi-restraints excluded: chain A residue 177 HIS 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 106 THR Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain C residue 350 VAL 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 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 102 ILE 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 118 THR 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 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: 0.9980 chunk 78 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 116 optimal weight: 0.2980 chunk 47 optimal weight: 0.2980 chunk 22 optimal weight: 0.0770 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 GLN C 450 ASN ** 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 = 0.3592 r_free = 0.3592 target = 0.125047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.109957 restraints weight = 14560.300| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.41 r_work: 0.3231 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10000 Z= 0.208 Angle : 0.672 10.747 13652 Z= 0.339 Chirality : 0.046 0.247 1498 Planarity : 0.005 0.043 1764 Dihedral : 7.010 77.900 1474 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.06 % Favored : 87.94 % Rotamer: Outliers : 4.14 % Allowed : 21.90 % Favored : 73.97 % 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: -2.76 (0.23), residues: 1252 helix: -5.03 (0.26), residues: 44 sheet: -1.16 (0.27), residues: 416 loop : -2.11 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 509 TYR 0.015 0.002 TYR C 508 PHE 0.018 0.002 PHE C 456 TRP 0.016 0.002 TRP F 436 HIS 0.008 0.001 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 9982) covalent geometry : angle 0.66862 (13614) SS BOND : bond 0.00443 ( 16) SS BOND : angle 1.02325 ( 32) hydrogen bonds : bond 0.03535 ( 174) hydrogen bonds : angle 5.99619 ( 447) link_NAG-ASN : bond 0.00282 ( 2) link_NAG-ASN : angle 2.63732 ( 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 257 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 213 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 25 SER cc_start: 0.8366 (t) cc_final: 0.8127 (m) REVERT: A 32 TYR cc_start: 0.8755 (m-80) cc_final: 0.8440 (m-80) REVERT: A 55 SER cc_start: 0.8240 (m) cc_final: 0.7700 (t) REVERT: A 85 SER cc_start: 0.8275 (t) cc_final: 0.7887 (t) REVERT: A 154 LEU cc_start: 0.8709 (tp) cc_final: 0.8327 (tp) REVERT: B 6 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7504 (mt0) REVERT: B 31 SER cc_start: 0.8577 (m) cc_final: 0.8241 (p) REVERT: B 76 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7791 (mpp80) REVERT: B 146 VAL cc_start: 0.8784 (t) cc_final: 0.8476 (p) REVERT: C 346 ARG cc_start: 0.8633 (mtt-85) cc_final: 0.8156 (mtt180) REVERT: C 350 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8236 (p) REVERT: C 360 ASN cc_start: 0.8325 (m110) cc_final: 0.8052 (m110) REVERT: C 425 LEU cc_start: 0.8511 (mt) cc_final: 0.8296 (mt) REVERT: C 448 ASN cc_start: 0.7857 (p0) cc_final: 0.7485 (p0) REVERT: C 481 ASN cc_start: 0.8457 (m-40) cc_final: 0.8143 (t0) REVERT: C 494 SER cc_start: 0.8392 (m) cc_final: 0.8140 (p) REVERT: C 518 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8327 (mp) REVERT: D 25 SER cc_start: 0.8759 (t) cc_final: 0.8382 (p) REVERT: D 126 SER cc_start: 0.8788 (m) cc_final: 0.8520 (p) REVERT: D 133 SER cc_start: 0.8505 (t) cc_final: 0.8146 (t) REVERT: D 137 LEU cc_start: 0.7593 (mt) cc_final: 0.7277 (mp) REVERT: E 51 SER cc_start: 0.8119 (m) cc_final: 0.7782 (p) REVERT: E 71 THR cc_start: 0.8355 (m) cc_final: 0.7967 (t) REVERT: E 81 ASP cc_start: 0.8351 (t70) cc_final: 0.8107 (t0) REVERT: E 147 THR cc_start: 0.8281 (m) cc_final: 0.7807 (p) REVERT: E 198 THR cc_start: 0.7762 (m) cc_final: 0.7496 (p) REVERT: F 386 LYS cc_start: 0.8510 (mmtt) cc_final: 0.8143 (mmtt) REVERT: F 438 SER cc_start: 0.8604 (m) cc_final: 0.8228 (p) outliers start: 44 outliers final: 35 residues processed: 240 average time/residue: 0.1011 time to fit residues: 33.6543 Evaluate side-chains 242 residues out of total 1066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 203 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 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 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 C residue 350 VAL 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 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 65 LYS 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 12 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 50 ASP 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 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: 0.2980 chunk 24 optimal weight: 0.0370 chunk 98 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 50 optimal weight: 0.4980 chunk 88 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 43 optimal weight: 0.4980 chunk 46 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3588 r_free = 0.3588 target = 0.124747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.109819 restraints weight = 14768.387| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.38 r_work: 0.3259 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10000 Z= 0.196 Angle : 0.672 10.928 13652 Z= 0.339 Chirality : 0.046 0.221 1498 Planarity : 0.005 0.057 1764 Dihedral : 7.113 78.365 1474 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.46 % Favored : 87.54 % Rotamer: Outliers : 3.95 % Allowed : 22.09 % Favored : 73.97 % 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: -2.75 (0.23), residues: 1252 helix: -4.98 (0.28), residues: 44 sheet: -1.07 (0.27), residues: 396 loop : -2.14 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 454 TYR 0.015 0.001 TYR C 508 PHE 0.017 0.002 PHE C 429 TRP 0.016 0.002 TRP D 167 HIS 0.007 0.001 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 9982) covalent geometry : angle 0.66935 (13614) SS BOND : bond 0.00405 ( 16) SS BOND : angle 0.99324 ( 32) hydrogen bonds : bond 0.03481 ( 174) hydrogen bonds : angle 6.03681 ( 447) link_NAG-ASN : bond 0.00218 ( 2) link_NAG-ASN : angle 2.50539 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2784.84 seconds wall clock time: 48 minutes 25.32 seconds (2905.32 seconds total)