Starting phenix.real_space_refine on Wed Sep 17 09:59:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ztf_60460/09_2025/8ztf_60460.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ztf_60460/09_2025/8ztf_60460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ztf_60460/09_2025/8ztf_60460.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ztf_60460/09_2025/8ztf_60460.map" model { file = "/net/cci-nas-00/data/ceres_data/8ztf_60460/09_2025/8ztf_60460.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ztf_60460/09_2025/8ztf_60460.cif" } resolution = 2.43 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= 0.002 sd= 0.054 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 P 9 5.49 5 Mg 3 5.21 5 S 45 5.16 5 C 5110 2.51 5 N 1358 2.21 5 O 1451 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7978 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2588 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 314} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2588 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 314} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2588 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 314} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 105 Unusual residues: {' MG': 1, 'ATP': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 76 Unusual residues: {' CA': 2, ' MG': 1, 'ATP': 1, 'NAG': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 1.97, per 1000 atoms: 0.25 Number of scatterers: 7978 At special positions: 0 Unit cell: (83.95, 87.6, 119.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 2 19.99 S 45 16.00 P 9 15.00 Mg 3 11.99 O 1451 8.00 N 1358 7.00 C 5110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 132 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 227 " distance=2.03 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 270 " distance=1.98 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=1.83 Simple disulfide: pdb=" SG CYS B 132 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 217 " - pdb=" SG CYS B 227 " distance=2.04 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 165 " distance=2.02 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 132 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 217 " - pdb=" SG CYS C 227 " distance=2.04 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 A 402 " - " ASN A 210 " " NAG A 403 " - " ASN A 153 " " NAG A 404 " - " ASN A 184 " " NAG B 503 " - " ASN B 210 " " NAG B 504 " - " ASN B 153 " " NAG B 505 " - " ASN B 184 " " NAG C 502 " - " ASN C 210 " " NAG C 503 " - " ASN C 153 " Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 316.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 17 sheets defined 27.1% alpha, 46.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 26 through 49 removed outlier: 3.690A pdb=" N PHE A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 179 through 184 removed outlier: 3.601A pdb=" N GLU A 183 " --> pdb=" O HIS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 217 removed outlier: 3.783A pdb=" N LYS A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 240 Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.581A pdb=" N LYS A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 355 Processing helix chain 'B' and resid 27 through 51 removed outlier: 4.744A pdb=" N VAL B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE B 49 " --> pdb=" O ILE B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 210 through 216 removed outlier: 3.562A pdb=" N LYS B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 240 removed outlier: 3.518A pdb=" N GLY B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.833A pdb=" N LYS B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 270 Processing helix chain 'B' and resid 327 through 355 removed outlier: 3.587A pdb=" N VAL B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 47 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 180 through 184 Processing helix chain 'C' and resid 232 through 239 Processing helix chain 'C' and resid 242 through 250 removed outlier: 4.047A pdb=" N GLU C 248 " --> pdb=" O ARG C 244 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYS C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 270 Processing helix chain 'C' and resid 327 through 355 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58 removed outlier: 3.724A pdb=" N LYS A 325 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL A 252 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 112 removed outlier: 5.321A pdb=" N VAL A 101 " --> pdb=" O PHE A 315 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N PHE A 315 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N MET A 103 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE A 313 " --> pdb=" O MET A 103 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN A 111 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ARG A 305 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 62 through 70 removed outlier: 3.519A pdb=" N VAL A 200 " --> pdb=" O PHE A 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 62 through 70 Processing sheet with id=AA5, first strand: chain 'A' and resid 73 through 75 Processing sheet with id=AA6, first strand: chain 'A' and resid 114 through 118 removed outlier: 5.127A pdb=" N ASN A 148 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N PHE A 162 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N THR A 146 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 9.399A pdb=" N TRP A 164 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 9.375A pdb=" N ILE A 144 " --> pdb=" O TRP A 164 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 56 through 57 removed outlier: 3.654A pdb=" N LYS B 325 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL B 252 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 100 through 112 removed outlier: 5.308A pdb=" N VAL B 101 " --> pdb=" O PHE B 315 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N PHE B 315 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N MET B 103 " --> pdb=" O ILE B 313 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE B 313 " --> pdb=" O MET B 103 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 307 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN B 111 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ARG B 305 " --> pdb=" O GLN B 111 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 62 through 70 removed outlier: 3.537A pdb=" N SER B 64 " --> pdb=" O SER B 192 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 192 " --> pdb=" O SER B 64 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 62 through 70 removed outlier: 3.537A pdb=" N SER B 64 " --> pdb=" O SER B 192 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 192 " --> pdb=" O SER B 64 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 73 through 75 Processing sheet with id=AB3, first strand: chain 'B' and resid 114 through 118 removed outlier: 5.124A pdb=" N ASN B 148 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N PHE B 162 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N THR B 146 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 9.463A pdb=" N TRP B 164 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N ILE B 144 " --> pdb=" O TRP B 164 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 56 through 60 removed outlier: 3.735A pdb=" N LYS C 325 " --> pdb=" O THR C 57 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA C 323 " --> pdb=" O SER C 59 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY C 251 " --> pdb=" O ARG C 314 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ASP C 316 " --> pdb=" O GLY C 251 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL C 253 " --> pdb=" O ASP C 316 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N LEU C 318 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE C 255 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ASP C 320 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE C 257 " --> pdb=" O ASP C 320 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N LYS C 322 " --> pdb=" O ILE C 257 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N TRP C 259 " --> pdb=" O LYS C 322 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N GLY C 324 " --> pdb=" O TRP C 259 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N CYS C 261 " --> pdb=" O GLY C 324 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N PHE C 326 " --> pdb=" O CYS C 261 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL C 252 " --> pdb=" O LEU C 279 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 135 through 136 removed outlier: 9.770A pdb=" N ILE C 144 " --> pdb=" O TRP C 164 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N TRP C 164 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N THR C 146 " --> pdb=" O PHE C 162 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N PHE C 162 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ASN C 148 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N SER C 99 " --> pdb=" O ILE C 317 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ILE C 317 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N VAL C 101 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N PHE C 315 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N MET C 103 " --> pdb=" O ILE C 313 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE C 313 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN C 111 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ARG C 305 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ALA C 113 " --> pdb=" O ASN C 303 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N ASN C 303 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 62 through 70 removed outlier: 3.635A pdb=" N THR C 186 " --> pdb=" O LYS C 70 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 200 " --> pdb=" O PHE C 195 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 62 through 70 removed outlier: 3.635A pdb=" N THR C 186 " --> pdb=" O LYS C 70 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 73 through 76 379 hydrogen bonds defined for protein. 1026 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: 0.98 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2223 1.33 - 1.45: 1563 1.45 - 1.58: 4318 1.58 - 1.70: 15 1.70 - 1.82: 57 Bond restraints: 8176 Sorted by residual: bond pdb=" C4 ATP A 405 " pdb=" C5 ATP A 405 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.45e+01 bond pdb=" C4 ATP B 502 " pdb=" C5 ATP B 502 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.40e+01 bond pdb=" C4 ATP A 401 " pdb=" C5 ATP A 401 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.28e+01 bond pdb=" C5 ATP A 405 " pdb=" C6 ATP A 405 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.86e+01 bond pdb=" C5 ATP B 502 " pdb=" C6 ATP B 502 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.86e+01 ... (remaining 8171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.57: 10955 3.57 - 7.14: 123 7.14 - 10.71: 18 10.71 - 14.28: 3 14.28 - 17.85: 3 Bond angle restraints: 11102 Sorted by residual: angle pdb=" PB ATP B 502 " pdb=" O3B ATP B 502 " pdb=" PG ATP B 502 " ideal model delta sigma weight residual 139.87 122.02 17.85 1.00e+00 1.00e+00 3.19e+02 angle pdb=" PB ATP A 401 " pdb=" O3B ATP A 401 " pdb=" PG ATP A 401 " ideal model delta sigma weight residual 139.87 122.54 17.33 1.00e+00 1.00e+00 3.00e+02 angle pdb=" PB ATP A 405 " pdb=" O3B ATP A 405 " pdb=" PG ATP A 405 " ideal model delta sigma weight residual 139.87 123.08 16.79 1.00e+00 1.00e+00 2.82e+02 angle pdb=" PA ATP B 502 " pdb=" O3A ATP B 502 " pdb=" PB ATP B 502 " ideal model delta sigma weight residual 136.83 123.10 13.73 1.00e+00 1.00e+00 1.88e+02 angle pdb=" PA ATP A 405 " pdb=" O3A ATP A 405 " pdb=" PB ATP A 405 " ideal model delta sigma weight residual 136.83 123.21 13.62 1.00e+00 1.00e+00 1.85e+02 ... (remaining 11097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.02: 4792 23.02 - 46.04: 114 46.04 - 69.06: 24 69.06 - 92.08: 7 92.08 - 115.10: 1 Dihedral angle restraints: 4938 sinusoidal: 2148 harmonic: 2790 Sorted by residual: dihedral pdb=" CB CYS A 261 " pdb=" SG CYS A 261 " pdb=" SG CYS A 270 " pdb=" CB CYS A 270 " ideal model delta sinusoidal sigma weight residual -86.00 -154.19 68.19 1 1.00e+01 1.00e-02 6.03e+01 dihedral pdb=" CB CYS A 117 " pdb=" SG CYS A 117 " pdb=" SG CYS A 165 " pdb=" CB CYS A 165 " ideal model delta sinusoidal sigma weight residual -86.00 -151.65 65.65 1 1.00e+01 1.00e-02 5.64e+01 dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual -86.00 -139.42 53.42 1 1.00e+01 1.00e-02 3.88e+01 ... (remaining 4935 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 1180 0.116 - 0.232: 47 0.232 - 0.348: 7 0.348 - 0.464: 1 0.464 - 0.581: 2 Chirality restraints: 1237 Sorted by residual: chirality pdb=" C1 NAG B 505 " pdb=" ND2 ASN B 184 " pdb=" C2 NAG B 505 " pdb=" O5 NAG B 505 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.43e+00 chirality pdb=" CA CYS A 165 " pdb=" N CYS A 165 " pdb=" C CYS A 165 " pdb=" CB CYS A 165 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.15e+00 chirality pdb=" CA PHE C 185 " pdb=" N PHE C 185 " pdb=" C PHE C 185 " pdb=" CB PHE C 185 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.57e+00 ... (remaining 1234 not shown) Planarity restraints: 1405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 404 " 0.263 2.00e-02 2.50e+03 2.22e-01 6.14e+02 pdb=" C7 NAG A 404 " -0.068 2.00e-02 2.50e+03 pdb=" C8 NAG A 404 " 0.174 2.00e-02 2.50e+03 pdb=" N2 NAG A 404 " -0.377 2.00e-02 2.50e+03 pdb=" O7 NAG A 404 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 505 " -0.113 2.00e-02 2.50e+03 9.29e-02 1.08e+02 pdb=" C7 NAG B 505 " 0.030 2.00e-02 2.50e+03 pdb=" C8 NAG B 505 " -0.085 2.00e-02 2.50e+03 pdb=" N2 NAG B 505 " 0.148 2.00e-02 2.50e+03 pdb=" O7 NAG B 505 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 204 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.12e+00 pdb=" C ASN A 204 " -0.046 2.00e-02 2.50e+03 pdb=" O ASN A 204 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU A 205 " 0.016 2.00e-02 2.50e+03 ... (remaining 1402 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2121 2.81 - 3.33: 7017 3.33 - 3.86: 13518 3.86 - 4.38: 15580 4.38 - 4.90: 26988 Nonbonded interactions: 65224 Sorted by model distance: nonbonded pdb=" O ILE C 189 " pdb=" ND2 ASN C 204 " model vdw 2.288 3.120 nonbonded pdb=" O VAL B 298 " pdb=" O HOH B 601 " model vdw 2.334 3.040 nonbonded pdb=" O PHE C 33 " pdb=" NE2 GLN C 37 " model vdw 2.345 3.120 nonbonded pdb=" NZ LYS B 190 " pdb=" O GLY C 288 " model vdw 2.363 3.120 nonbonded pdb=" O VAL A 298 " pdb=" O HOH B 601 " model vdw 2.383 3.040 ... (remaining 65219 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 355 or resid 403)) selection = (chain 'B' and (resid 26 through 355 or resid 503)) selection = (chain 'C' and (resid 26 through 355 or resid 503)) } 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.760 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 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 : 0.005 0.201 8197 Z= 0.399 Angle : 0.971 17.852 11152 Z= 0.689 Chirality : 0.061 0.581 1237 Planarity : 0.008 0.222 1397 Dihedral : 10.647 115.104 3123 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.77 % Allowed : 3.66 % Favored : 94.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 aren not related in a simple way. whole: -0.26 (0.25), residues: 984 helix: -0.39 (0.31), residues: 273 sheet: 1.23 (0.30), residues: 264 loop : -0.84 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 292 TYR 0.012 0.001 TYR A 213 PHE 0.012 0.001 PHE A 291 TRP 0.015 0.001 TRP A 259 HIS 0.004 0.000 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 8176) covalent geometry : angle 0.94194 (11102) SS BOND : bond 0.05803 ( 13) SS BOND : angle 4.16123 ( 26) hydrogen bonds : bond 0.23255 ( 352) hydrogen bonds : angle 8.65702 ( 1026) link_NAG-ASN : bond 0.01021 ( 8) link_NAG-ASN : angle 3.05787 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 178 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 4 residues processed: 192 average time/residue: 0.5989 time to fit residues: 120.8886 Evaluate side-chains 108 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 258 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 50.0000 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 116 HIS A 191 ASN A 220 HIS A 241 GLN A 290 ASN A 303 ASN B 191 ASN B 220 HIS C 56 GLN C 114 GLN C 191 ASN C 220 HIS C 290 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.132220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.100656 restraints weight = 11508.421| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.63 r_work: 0.3282 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8197 Z= 0.174 Angle : 0.623 9.568 11152 Z= 0.327 Chirality : 0.047 0.221 1237 Planarity : 0.005 0.032 1397 Dihedral : 9.266 89.911 1334 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.55 % Allowed : 12.41 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 aren not related in a simple way. whole: 0.71 (0.26), residues: 984 helix: 0.89 (0.33), residues: 258 sheet: 1.10 (0.28), residues: 297 loop : -0.15 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 197 TYR 0.028 0.002 TYR C 90 PHE 0.020 0.002 PHE C 92 TRP 0.013 0.001 TRP A 164 HIS 0.004 0.001 HIS B 95 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 8176) covalent geometry : angle 0.61059 (11102) SS BOND : bond 0.00688 ( 13) SS BOND : angle 1.86918 ( 26) hydrogen bonds : bond 0.03814 ( 352) hydrogen bonds : angle 5.51878 ( 1026) link_NAG-ASN : bond 0.00497 ( 8) link_NAG-ASN : angle 2.06671 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 LYS cc_start: 0.8475 (mtpp) cc_final: 0.8262 (mtmt) REVERT: A 258 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.7946 (t70) REVERT: A 318 LEU cc_start: 0.8755 (mp) cc_final: 0.8485 (mm) REVERT: B 80 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7300 (tt) outliers start: 30 outliers final: 15 residues processed: 120 average time/residue: 0.5562 time to fit residues: 70.7316 Evaluate side-chains 101 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 275 GLN Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 203 ARG Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 337 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 93 optimal weight: 0.0980 chunk 51 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.130639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.099387 restraints weight = 11431.375| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.60 r_work: 0.3271 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8197 Z= 0.123 Angle : 0.546 7.348 11152 Z= 0.284 Chirality : 0.045 0.199 1237 Planarity : 0.004 0.030 1397 Dihedral : 8.589 78.600 1332 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.26 % Allowed : 13.48 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 aren not related in a simple way. whole: 0.93 (0.27), residues: 984 helix: 1.40 (0.34), residues: 258 sheet: 1.05 (0.29), residues: 297 loop : -0.10 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 292 TYR 0.018 0.001 TYR A 90 PHE 0.020 0.001 PHE C 92 TRP 0.008 0.001 TRP A 164 HIS 0.007 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8176) covalent geometry : angle 0.53336 (11102) SS BOND : bond 0.00273 ( 13) SS BOND : angle 1.47822 ( 26) hydrogen bonds : bond 0.03285 ( 352) hydrogen bonds : angle 4.95754 ( 1026) link_NAG-ASN : bond 0.00418 ( 8) link_NAG-ASN : angle 2.10573 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 95 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7815 (mp0) cc_final: 0.7541 (mp0) REVERT: A 258 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8132 (t70) REVERT: A 303 ASN cc_start: 0.8636 (m110) cc_final: 0.8428 (t0) REVERT: A 318 LEU cc_start: 0.8773 (mp) cc_final: 0.8462 (mm) REVERT: B 80 LEU cc_start: 0.7766 (tp) cc_final: 0.7527 (tt) REVERT: B 127 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8535 (mp10) REVERT: B 248 GLU cc_start: 0.8492 (tt0) cc_final: 0.8047 (mm-30) REVERT: B 348 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8207 (mp) REVERT: C 62 ILE cc_start: 0.8726 (mm) cc_final: 0.8469 (pt) REVERT: C 199 LYS cc_start: 0.9064 (mtpm) cc_final: 0.8694 (mttp) REVERT: C 244 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8183 (ttm170) outliers start: 36 outliers final: 18 residues processed: 124 average time/residue: 0.5542 time to fit residues: 72.6298 Evaluate side-chains 105 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 275 GLN Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 337 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 82 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS B 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.126414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.094342 restraints weight = 11753.783| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.59 r_work: 0.3161 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8197 Z= 0.166 Angle : 0.604 11.023 11152 Z= 0.318 Chirality : 0.046 0.202 1237 Planarity : 0.004 0.032 1397 Dihedral : 8.695 77.238 1332 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.85 % Allowed : 14.66 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 aren not related in a simple way. whole: 0.99 (0.27), residues: 984 helix: 1.56 (0.34), residues: 255 sheet: 1.00 (0.29), residues: 297 loop : -0.07 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 197 TYR 0.019 0.002 TYR B 90 PHE 0.028 0.002 PHE C 92 TRP 0.008 0.001 TRP B 259 HIS 0.008 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 8176) covalent geometry : angle 0.58292 (11102) SS BOND : bond 0.00775 ( 13) SS BOND : angle 2.82188 ( 26) hydrogen bonds : bond 0.03240 ( 352) hydrogen bonds : angle 4.77669 ( 1026) link_NAG-ASN : bond 0.00423 ( 8) link_NAG-ASN : angle 1.89445 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 84 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LYS cc_start: 0.8437 (tptt) cc_final: 0.8144 (tppp) REVERT: A 197 ARG cc_start: 0.8874 (mtp-110) cc_final: 0.8649 (mtm110) REVERT: A 258 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.8188 (t70) REVERT: A 275 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8039 (mt0) REVERT: A 303 ASN cc_start: 0.8701 (m110) cc_final: 0.8425 (t0) REVERT: A 318 LEU cc_start: 0.8739 (mp) cc_final: 0.8440 (mm) REVERT: B 80 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7492 (tt) REVERT: B 348 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8181 (mp) outliers start: 41 outliers final: 20 residues processed: 116 average time/residue: 0.5671 time to fit residues: 70.0364 Evaluate side-chains 103 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 275 GLN Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 275 GLN Chi-restraints excluded: chain C residue 337 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 14 optimal weight: 0.0980 chunk 0 optimal weight: 40.0000 chunk 94 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.123616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.090848 restraints weight = 11506.300| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.58 r_work: 0.3117 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8197 Z= 0.181 Angle : 0.612 9.294 11152 Z= 0.324 Chirality : 0.047 0.223 1237 Planarity : 0.004 0.042 1397 Dihedral : 8.717 73.461 1330 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.85 % Allowed : 14.89 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.27), residues: 984 helix: 1.19 (0.34), residues: 273 sheet: 0.97 (0.30), residues: 279 loop : -0.34 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 197 TYR 0.021 0.002 TYR C 90 PHE 0.033 0.002 PHE C 92 TRP 0.009 0.001 TRP A 47 HIS 0.003 0.001 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 8176) covalent geometry : angle 0.59353 (11102) SS BOND : bond 0.00441 ( 13) SS BOND : angle 2.68971 ( 26) hydrogen bonds : bond 0.03242 ( 352) hydrogen bonds : angle 4.75253 ( 1026) link_NAG-ASN : bond 0.00572 ( 8) link_NAG-ASN : angle 1.73803 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 82 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LYS cc_start: 0.8495 (tptt) cc_final: 0.8190 (tppp) REVERT: A 258 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8227 (t70) REVERT: A 275 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8109 (mt0) REVERT: A 318 LEU cc_start: 0.8764 (mp) cc_final: 0.8463 (mm) REVERT: B 80 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7535 (tt) REVERT: B 216 LYS cc_start: 0.8437 (mttp) cc_final: 0.7904 (pmmt) REVERT: C 103 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8936 (ttt) REVERT: C 108 MET cc_start: 0.9022 (ttt) cc_final: 0.8744 (ttt) REVERT: C 197 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8209 (ttp-170) REVERT: C 322 LYS cc_start: 0.8749 (ptmm) cc_final: 0.8420 (ptpp) outliers start: 41 outliers final: 19 residues processed: 114 average time/residue: 0.5203 time to fit residues: 63.3420 Evaluate side-chains 102 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 275 GLN Chi-restraints excluded: chain C residue 337 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS ** C 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.124774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.092248 restraints weight = 11378.392| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.59 r_work: 0.3129 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8197 Z= 0.131 Angle : 0.613 12.007 11152 Z= 0.319 Chirality : 0.046 0.201 1237 Planarity : 0.004 0.049 1397 Dihedral : 8.528 72.074 1330 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.66 % Allowed : 15.48 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.27), residues: 984 helix: 1.24 (0.34), residues: 273 sheet: 0.94 (0.30), residues: 279 loop : -0.34 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 197 TYR 0.019 0.001 TYR B 43 PHE 0.026 0.002 PHE C 92 TRP 0.008 0.001 TRP B 259 HIS 0.002 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8176) covalent geometry : angle 0.57978 (11102) SS BOND : bond 0.00271 ( 13) SS BOND : angle 3.83057 ( 26) hydrogen bonds : bond 0.02924 ( 352) hydrogen bonds : angle 4.66822 ( 1026) link_NAG-ASN : bond 0.00650 ( 8) link_NAG-ASN : angle 1.82437 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 78 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LYS cc_start: 0.8511 (tptt) cc_final: 0.8213 (tppp) REVERT: A 197 ARG cc_start: 0.8975 (mtp-110) cc_final: 0.8699 (mtp85) REVERT: A 258 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8205 (t70) REVERT: A 275 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8018 (mt0) REVERT: A 303 ASN cc_start: 0.8659 (m110) cc_final: 0.8402 (t0) REVERT: B 80 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7573 (tt) REVERT: B 197 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8332 (ttp80) REVERT: B 210 ASN cc_start: 0.7897 (OUTLIER) cc_final: 0.7500 (p0) REVERT: B 216 LYS cc_start: 0.8436 (mttp) cc_final: 0.7908 (pmmt) REVERT: C 62 ILE cc_start: 0.8754 (mm) cc_final: 0.8511 (pt) REVERT: C 108 MET cc_start: 0.8977 (ttt) cc_final: 0.8679 (ttt) REVERT: C 197 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8196 (ttp-170) REVERT: C 210 ASN cc_start: 0.7965 (OUTLIER) cc_final: 0.7699 (p0) REVERT: C 322 LYS cc_start: 0.8718 (ptmm) cc_final: 0.8403 (ptpp) outliers start: 31 outliers final: 16 residues processed: 99 average time/residue: 0.5349 time to fit residues: 56.3636 Evaluate side-chains 97 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 117 CYS Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 275 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 31 optimal weight: 9.9990 chunk 39 optimal weight: 0.0980 chunk 28 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.124434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.091934 restraints weight = 11401.968| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.57 r_work: 0.3122 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8197 Z= 0.140 Angle : 0.608 10.619 11152 Z= 0.315 Chirality : 0.046 0.199 1237 Planarity : 0.004 0.041 1397 Dihedral : 8.569 72.900 1330 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.66 % Allowed : 16.19 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.27), residues: 984 helix: 1.30 (0.34), residues: 273 sheet: 0.94 (0.29), residues: 279 loop : -0.35 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 197 TYR 0.017 0.001 TYR C 90 PHE 0.028 0.002 PHE C 92 TRP 0.009 0.001 TRP B 259 HIS 0.002 0.001 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 8176) covalent geometry : angle 0.58422 (11102) SS BOND : bond 0.00323 ( 13) SS BOND : angle 3.21216 ( 26) hydrogen bonds : bond 0.02959 ( 352) hydrogen bonds : angle 4.62410 ( 1026) link_NAG-ASN : bond 0.00737 ( 8) link_NAG-ASN : angle 1.59737 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 72 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LYS cc_start: 0.8532 (tptt) cc_final: 0.8220 (tppp) REVERT: A 197 ARG cc_start: 0.8994 (mtp-110) cc_final: 0.8670 (mtp85) REVERT: A 275 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8015 (mt0) REVERT: A 303 ASN cc_start: 0.8662 (m110) cc_final: 0.8423 (t0) REVERT: B 80 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7647 (tt) REVERT: B 159 CYS cc_start: 0.6641 (OUTLIER) cc_final: 0.4963 (m) REVERT: B 197 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8319 (ttp80) REVERT: B 210 ASN cc_start: 0.7931 (OUTLIER) cc_final: 0.7535 (p0) REVERT: B 216 LYS cc_start: 0.8449 (mttp) cc_final: 0.7966 (pmmt) REVERT: C 197 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8207 (ttp-170) REVERT: C 210 ASN cc_start: 0.7989 (OUTLIER) cc_final: 0.7723 (p0) REVERT: C 322 LYS cc_start: 0.8681 (ptmm) cc_final: 0.8374 (ptpp) outliers start: 31 outliers final: 19 residues processed: 97 average time/residue: 0.4944 time to fit residues: 51.2753 Evaluate side-chains 97 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 117 CYS Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 159 CYS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 275 GLN Chi-restraints excluded: chain C residue 337 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 87 optimal weight: 0.4980 chunk 21 optimal weight: 0.3980 chunk 51 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.124856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.092442 restraints weight = 11558.173| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.63 r_work: 0.3147 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8197 Z= 0.108 Angle : 0.566 8.282 11152 Z= 0.296 Chirality : 0.045 0.195 1237 Planarity : 0.004 0.033 1397 Dihedral : 8.196 69.846 1330 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.19 % Allowed : 16.78 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.27), residues: 984 helix: 1.34 (0.34), residues: 273 sheet: 0.84 (0.29), residues: 291 loop : -0.28 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 197 TYR 0.022 0.001 TYR B 43 PHE 0.020 0.001 PHE C 92 TRP 0.009 0.001 TRP B 164 HIS 0.001 0.000 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 8176) covalent geometry : angle 0.54232 (11102) SS BOND : bond 0.00281 ( 13) SS BOND : angle 3.14522 ( 26) hydrogen bonds : bond 0.02676 ( 352) hydrogen bonds : angle 4.55443 ( 1026) link_NAG-ASN : bond 0.00574 ( 8) link_NAG-ASN : angle 1.49448 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 THR cc_start: 0.9102 (m) cc_final: 0.8801 (p) REVERT: A 172 LYS cc_start: 0.8515 (tptt) cc_final: 0.8191 (tppp) REVERT: A 197 ARG cc_start: 0.8953 (mtp-110) cc_final: 0.8630 (mtp85) REVERT: A 275 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7959 (mt0) REVERT: B 80 LEU cc_start: 0.7886 (tp) cc_final: 0.7639 (tt) REVERT: B 159 CYS cc_start: 0.6438 (OUTLIER) cc_final: 0.5352 (m) REVERT: B 210 ASN cc_start: 0.7898 (OUTLIER) cc_final: 0.7507 (p0) REVERT: B 216 LYS cc_start: 0.8436 (mttp) cc_final: 0.7943 (pmmt) REVERT: C 210 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7730 (p0) REVERT: C 322 LYS cc_start: 0.8678 (ptmm) cc_final: 0.8441 (ptpp) outliers start: 27 outliers final: 12 residues processed: 96 average time/residue: 0.5120 time to fit residues: 52.4892 Evaluate side-chains 91 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 117 CYS Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 159 CYS Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 275 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 13 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.125650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.094225 restraints weight = 11622.972| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.52 r_work: 0.3196 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8197 Z= 0.133 Angle : 0.587 9.537 11152 Z= 0.306 Chirality : 0.045 0.215 1237 Planarity : 0.004 0.032 1397 Dihedral : 8.291 71.919 1330 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.48 % Allowed : 17.49 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.27), residues: 984 helix: 1.28 (0.34), residues: 276 sheet: 0.86 (0.30), residues: 273 loop : -0.30 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 197 TYR 0.016 0.001 TYR C 90 PHE 0.025 0.002 PHE C 92 TRP 0.008 0.001 TRP B 259 HIS 0.002 0.001 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8176) covalent geometry : angle 0.56418 (11102) SS BOND : bond 0.00306 ( 13) SS BOND : angle 3.12654 ( 26) hydrogen bonds : bond 0.02829 ( 352) hydrogen bonds : angle 4.54370 ( 1026) link_NAG-ASN : bond 0.00553 ( 8) link_NAG-ASN : angle 1.45137 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 THR cc_start: 0.9141 (m) cc_final: 0.8847 (p) REVERT: A 172 LYS cc_start: 0.8602 (tptt) cc_final: 0.8288 (tppp) REVERT: A 197 ARG cc_start: 0.8989 (mtp-110) cc_final: 0.8674 (mtp85) REVERT: A 275 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8109 (mt0) REVERT: B 80 LEU cc_start: 0.7948 (tp) cc_final: 0.7712 (tt) REVERT: B 210 ASN cc_start: 0.7992 (OUTLIER) cc_final: 0.7605 (p0) REVERT: B 216 LYS cc_start: 0.8458 (mttp) cc_final: 0.8004 (pmmt) REVERT: C 210 ASN cc_start: 0.8045 (OUTLIER) cc_final: 0.7798 (p0) REVERT: C 322 LYS cc_start: 0.8776 (ptmm) cc_final: 0.8464 (ptpp) outliers start: 21 outliers final: 14 residues processed: 91 average time/residue: 0.5033 time to fit residues: 48.8269 Evaluate side-chains 89 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 117 CYS Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 275 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 89 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 83 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.122606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.090365 restraints weight = 11566.371| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.56 r_work: 0.3090 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8197 Z= 0.172 Angle : 0.626 9.396 11152 Z= 0.329 Chirality : 0.047 0.220 1237 Planarity : 0.004 0.031 1397 Dihedral : 8.740 76.962 1330 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.48 % Allowed : 17.73 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.27), residues: 984 helix: 1.35 (0.35), residues: 258 sheet: 0.92 (0.29), residues: 279 loop : -0.44 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 197 TYR 0.026 0.002 TYR B 43 PHE 0.032 0.002 PHE C 92 TRP 0.010 0.001 TRP C 47 HIS 0.003 0.001 HIS B 220 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 8176) covalent geometry : angle 0.60224 (11102) SS BOND : bond 0.00412 ( 13) SS BOND : angle 3.35981 ( 26) hydrogen bonds : bond 0.03110 ( 352) hydrogen bonds : angle 4.64085 ( 1026) link_NAG-ASN : bond 0.00564 ( 8) link_NAG-ASN : angle 1.49167 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LYS cc_start: 0.8568 (tptt) cc_final: 0.8271 (tppp) REVERT: A 197 ARG cc_start: 0.8978 (mtp-110) cc_final: 0.8693 (mtp85) REVERT: A 208 GLU cc_start: 0.8185 (mp0) cc_final: 0.7886 (mp0) REVERT: A 275 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8045 (mt0) REVERT: B 80 LEU cc_start: 0.7922 (tp) cc_final: 0.7682 (tt) REVERT: B 197 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8331 (ttp80) REVERT: B 210 ASN cc_start: 0.7936 (OUTLIER) cc_final: 0.7569 (p0) REVERT: B 216 LYS cc_start: 0.8501 (mttp) cc_final: 0.8088 (pmmt) REVERT: C 210 ASN cc_start: 0.8053 (OUTLIER) cc_final: 0.7788 (p0) REVERT: C 322 LYS cc_start: 0.8715 (ptmm) cc_final: 0.8407 (ptpp) outliers start: 21 outliers final: 14 residues processed: 90 average time/residue: 0.5053 time to fit residues: 48.7330 Evaluate side-chains 91 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 117 CYS Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 210 ASN Chi-restraints excluded: chain C residue 258 ASP Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 275 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 95 optimal weight: 0.0670 chunk 13 optimal weight: 0.3980 chunk 72 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 0 optimal weight: 40.0000 chunk 27 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 120 ASN ** 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 = 0.3704 r_free = 0.3704 target = 0.124452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.091811 restraints weight = 11384.314| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.59 r_work: 0.3156 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8197 Z= 0.111 Angle : 0.611 12.872 11152 Z= 0.318 Chirality : 0.045 0.213 1237 Planarity : 0.004 0.032 1397 Dihedral : 8.418 73.015 1330 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.48 % Allowed : 18.09 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.27), residues: 984 helix: 1.39 (0.35), residues: 258 sheet: 0.83 (0.30), residues: 273 loop : -0.42 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 197 TYR 0.021 0.001 TYR B 43 PHE 0.022 0.001 PHE C 92 TRP 0.010 0.001 TRP B 164 HIS 0.002 0.000 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8176) covalent geometry : angle 0.57480 (11102) SS BOND : bond 0.00339 ( 13) SS BOND : angle 4.12800 ( 26) hydrogen bonds : bond 0.02693 ( 352) hydrogen bonds : angle 4.54915 ( 1026) link_NAG-ASN : bond 0.00529 ( 8) link_NAG-ASN : angle 1.41302 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3435.19 seconds wall clock time: 59 minutes 8.00 seconds (3548.00 seconds total)