Starting phenix.real_space_refine on Fri Jul 25 17:52:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ztf_60460/07_2025/8ztf_60460.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ztf_60460/07_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_60460/07_2025/8ztf_60460.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ztf_60460/07_2025/8ztf_60460.map" model { file = "/net/cci-nas-00/data/ceres_data/8ztf_60460/07_2025/8ztf_60460.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ztf_60460/07_2025/8ztf_60460.cif" } resolution = 2.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.66, per 1000 atoms: 0.71 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: 2.20 Conformation dependent library (CDL) restraints added in 963.7 milliseconds 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: 1.00 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: 2.34 Time building geometry restraints manager: 2.58 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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.690 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.960 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.015 0.001 TRP A 259 HIS 0.004 0.000 HIS A 116 PHE 0.012 0.001 PHE A 291 TYR 0.012 0.001 TYR A 213 ARG 0.004 0.000 ARG A 292 Details of bonding type rmsd link_NAG-ASN : bond 0.01021 ( 8) link_NAG-ASN : angle 3.05787 ( 24) hydrogen bonds : bond 0.23255 ( 352) hydrogen bonds : angle 8.65702 ( 1026) SS BOND : bond 0.05803 ( 13) SS BOND : angle 4.16123 ( 26) covalent geometry : bond 0.00495 ( 8176) covalent geometry : angle 0.94194 (11102) *********************** 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 : 0.910 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: 1.2846 time to fit residues: 259.9925 Evaluate side-chains 107 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 83 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 77 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 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 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 = 0.3844 r_free = 0.3844 target = 0.135822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.104971 restraints weight = 11366.190| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.62 r_work: 0.3353 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8197 Z= 0.136 Angle : 0.603 8.951 11152 Z= 0.315 Chirality : 0.046 0.216 1237 Planarity : 0.005 0.034 1397 Dihedral : 9.221 88.451 1334 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.72 % Allowed : 13.12 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 984 helix: 0.88 (0.33), residues: 258 sheet: 1.21 (0.29), residues: 279 loop : -0.23 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 47 HIS 0.003 0.001 HIS A 116 PHE 0.017 0.002 PHE B 243 TYR 0.025 0.002 TYR C 90 ARG 0.006 0.001 ARG A 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 8) link_NAG-ASN : angle 2.02687 ( 24) hydrogen bonds : bond 0.03745 ( 352) hydrogen bonds : angle 5.70977 ( 1026) SS BOND : bond 0.00487 ( 13) SS BOND : angle 2.02795 ( 26) covalent geometry : bond 0.00293 ( 8176) covalent geometry : angle 0.58841 (11102) *********************** 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 126 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.971 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 258 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7897 (t70) REVERT: A 303 ASN cc_start: 0.8622 (m110) cc_final: 0.8406 (t0) REVERT: A 318 LEU cc_start: 0.8761 (mp) cc_final: 0.8495 (mm) REVERT: B 80 LEU cc_start: 0.7740 (tp) cc_final: 0.7333 (tt) outliers start: 23 outliers final: 13 residues processed: 120 average time/residue: 1.1733 time to fit residues: 150.0287 Evaluate side-chains 101 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 9 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 33 optimal weight: 40.0000 chunk 40 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN A 116 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.128159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.096308 restraints weight = 11482.210| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.60 r_work: 0.3221 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8197 Z= 0.143 Angle : 0.569 7.304 11152 Z= 0.297 Chirality : 0.046 0.204 1237 Planarity : 0.004 0.032 1397 Dihedral : 8.712 79.079 1332 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.02 % Allowed : 14.18 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.27), residues: 984 helix: 1.55 (0.35), residues: 240 sheet: 1.02 (0.28), residues: 297 loop : -0.07 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.004 0.001 HIS A 116 PHE 0.024 0.002 PHE C 92 TYR 0.021 0.001 TYR C 90 ARG 0.004 0.001 ARG A 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00424 ( 8) link_NAG-ASN : angle 2.11061 ( 24) hydrogen bonds : bond 0.03453 ( 352) hydrogen bonds : angle 4.93648 ( 1026) SS BOND : bond 0.00254 ( 13) SS BOND : angle 1.62732 ( 26) covalent geometry : bond 0.00325 ( 8176) covalent geometry : angle 0.55621 (11102) *********************** 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 125 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 91 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8126 (t70) REVERT: A 303 ASN cc_start: 0.8681 (m110) cc_final: 0.8412 (t0) REVERT: A 318 LEU cc_start: 0.8741 (mp) cc_final: 0.8419 (mm) REVERT: B 80 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7505 (tt) REVERT: B 127 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8544 (mp10) REVERT: B 248 GLU cc_start: 0.8378 (tt0) cc_final: 0.8037 (mm-30) REVERT: B 348 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8187 (mp) REVERT: C 62 ILE cc_start: 0.8716 (mm) cc_final: 0.8384 (pt) REVERT: C 244 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8215 (ttm170) outliers start: 34 outliers final: 17 residues processed: 115 average time/residue: 1.2012 time to fit residues: 146.7218 Evaluate side-chains 102 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER 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 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 348 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 37 GLN 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 46 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 72 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 98 optimal weight: 20.0000 chunk 65 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.124741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.092632 restraints weight = 11556.604| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.56 r_work: 0.3152 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3613 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= 0.195 Angle : 0.618 11.352 11152 Z= 0.326 Chirality : 0.047 0.204 1237 Planarity : 0.004 0.037 1397 Dihedral : 8.846 77.978 1332 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 5.44 % Allowed : 14.07 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.27), residues: 984 helix: 1.77 (0.36), residues: 231 sheet: 0.83 (0.29), residues: 288 loop : -0.10 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 47 HIS 0.010 0.001 HIS A 116 PHE 0.033 0.002 PHE C 92 TYR 0.019 0.002 TYR A 90 ARG 0.010 0.001 ARG A 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00417 ( 8) link_NAG-ASN : angle 1.90793 ( 24) hydrogen bonds : bond 0.03394 ( 352) hydrogen bonds : angle 4.80716 ( 1026) SS BOND : bond 0.00328 ( 13) SS BOND : angle 2.79888 ( 26) covalent geometry : bond 0.00446 ( 8176) covalent geometry : angle 0.59800 (11102) *********************** 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 131 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 85 time to evaluate : 0.921 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 61 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8908 (pp) REVERT: A 172 LYS cc_start: 0.8509 (tptt) cc_final: 0.8227 (tppp) REVERT: A 258 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8256 (t70) REVERT: A 275 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8118 (mt0) REVERT: A 318 LEU cc_start: 0.8787 (mp) cc_final: 0.8502 (mm) REVERT: B 80 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7556 (tt) REVERT: C 145 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8260 (mtt-85) REVERT: C 197 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.7948 (ttp-170) REVERT: C 322 LYS cc_start: 0.8767 (ptmm) cc_final: 0.8524 (ptpp) outliers start: 46 outliers final: 24 residues processed: 120 average time/residue: 1.0906 time to fit residues: 139.8115 Evaluate side-chains 107 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 63 SER 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 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 132 CYS 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 275 GLN 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 145 ARG 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 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 92 optimal weight: 1.9990 chunk 75 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 116 HIS ** C 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.126343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.093976 restraints weight = 11118.405| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.57 r_work: 0.3190 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3692 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= 0.118 Angle : 0.583 12.591 11152 Z= 0.305 Chirality : 0.045 0.204 1237 Planarity : 0.004 0.031 1397 Dihedral : 8.499 73.749 1332 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.14 % Allowed : 15.37 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.27), residues: 984 helix: 1.74 (0.35), residues: 240 sheet: 0.89 (0.30), residues: 273 loop : -0.09 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 164 HIS 0.003 0.001 HIS A 116 PHE 0.023 0.001 PHE C 92 TYR 0.019 0.001 TYR C 90 ARG 0.005 0.000 ARG A 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00418 ( 8) link_NAG-ASN : angle 1.73801 ( 24) hydrogen bonds : bond 0.02855 ( 352) hydrogen bonds : angle 4.65833 ( 1026) SS BOND : bond 0.00317 ( 13) SS BOND : angle 3.31621 ( 26) covalent geometry : bond 0.00263 ( 8176) covalent geometry : angle 0.55574 (11102) *********************** 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 118 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 83 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LYS cc_start: 0.8502 (tptt) cc_final: 0.8213 (tppp) REVERT: A 275 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8078 (mt0) REVERT: A 303 ASN cc_start: 0.8648 (m110) cc_final: 0.8422 (t0) REVERT: A 318 LEU cc_start: 0.8718 (mp) cc_final: 0.8381 (mm) REVERT: B 80 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7603 (tt) REVERT: C 62 ILE cc_start: 0.8762 (mm) cc_final: 0.8504 (pt) REVERT: C 197 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8122 (ttp-170) REVERT: C 203 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8663 (ttp-170) REVERT: C 244 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8317 (ttm170) REVERT: C 322 LYS cc_start: 0.8746 (ptmm) cc_final: 0.8405 (ptpp) outliers start: 35 outliers final: 15 residues processed: 112 average time/residue: 1.1684 time to fit residues: 139.3154 Evaluate side-chains 99 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 44 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 203 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 337 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 96 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.3675 r_free = 0.3675 target = 0.122082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.088716 restraints weight = 11505.291| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.59 r_work: 0.3105 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 8197 Z= 0.224 Angle : 0.660 9.843 11152 Z= 0.347 Chirality : 0.049 0.254 1237 Planarity : 0.005 0.045 1397 Dihedral : 9.032 77.095 1330 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.37 % Allowed : 15.25 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.27), residues: 984 helix: 1.20 (0.34), residues: 267 sheet: 0.77 (0.29), residues: 288 loop : -0.36 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 47 HIS 0.005 0.001 HIS C 269 PHE 0.037 0.002 PHE C 92 TYR 0.019 0.002 TYR C 90 ARG 0.011 0.001 ARG A 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 8) link_NAG-ASN : angle 1.65992 ( 24) hydrogen bonds : bond 0.03517 ( 352) hydrogen bonds : angle 4.80608 ( 1026) SS BOND : bond 0.00398 ( 13) SS BOND : angle 3.44686 ( 26) covalent geometry : bond 0.00519 ( 8176) covalent geometry : angle 0.63501 (11102) *********************** 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 118 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 81 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LYS cc_start: 0.8561 (tptt) cc_final: 0.8294 (tppp) REVERT: A 197 ARG cc_start: 0.8996 (mtp-110) cc_final: 0.8751 (mtp85) REVERT: A 258 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8243 (t70) REVERT: A 275 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8135 (mt0) REVERT: A 318 LEU cc_start: 0.8783 (mp) cc_final: 0.8487 (mm) REVERT: B 80 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7620 (tt) REVERT: B 197 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8341 (ttp80) REVERT: B 210 ASN cc_start: 0.7967 (OUTLIER) cc_final: 0.7569 (p0) REVERT: B 216 LYS cc_start: 0.8471 (mttp) cc_final: 0.8023 (pmmt) REVERT: C 197 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8285 (ttp-170) REVERT: C 322 LYS cc_start: 0.8750 (ptmm) cc_final: 0.8416 (ptpp) outliers start: 37 outliers final: 18 residues processed: 108 average time/residue: 1.0824 time to fit residues: 124.9028 Evaluate side-chains 99 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER 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 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 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 267 VAL Chi-restraints excluded: chain C residue 275 GLN Chi-restraints excluded: chain C residue 337 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 33 optimal weight: 50.0000 chunk 82 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 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 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.124640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.092314 restraints weight = 11453.192| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.58 r_work: 0.3137 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8197 Z= 0.122 Angle : 0.602 11.182 11152 Z= 0.315 Chirality : 0.046 0.200 1237 Planarity : 0.004 0.039 1397 Dihedral : 8.616 72.692 1330 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.43 % Allowed : 16.67 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.27), residues: 984 helix: 1.31 (0.35), residues: 258 sheet: 0.87 (0.30), residues: 279 loop : -0.38 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 259 HIS 0.002 0.000 HIS B 220 PHE 0.026 0.001 PHE C 92 TYR 0.020 0.001 TYR B 43 ARG 0.009 0.000 ARG A 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00713 ( 8) link_NAG-ASN : angle 1.84580 ( 24) hydrogen bonds : bond 0.02921 ( 352) hydrogen bonds : angle 4.67117 ( 1026) SS BOND : bond 0.00286 ( 13) SS BOND : angle 3.25627 ( 26) covalent geometry : bond 0.00271 ( 8176) covalent geometry : angle 0.57588 (11102) *********************** 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 104 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LYS cc_start: 0.8532 (tptt) cc_final: 0.8258 (tppp) REVERT: A 197 ARG cc_start: 0.8998 (mtp-110) cc_final: 0.8707 (mtp85) REVERT: A 275 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8034 (mt0) REVERT: A 303 ASN cc_start: 0.8664 (m-40) cc_final: 0.8401 (t0) REVERT: B 80 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7644 (tt) REVERT: B 197 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8298 (ttp80) REVERT: B 210 ASN cc_start: 0.7924 (OUTLIER) cc_final: 0.7550 (p0) REVERT: B 216 LYS cc_start: 0.8476 (mttp) cc_final: 0.7980 (pmmt) REVERT: C 197 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8208 (ttp-170) REVERT: C 210 ASN cc_start: 0.7980 (OUTLIER) cc_final: 0.7733 (p0) REVERT: C 322 LYS cc_start: 0.8704 (ptmm) cc_final: 0.8394 (ptpp) outliers start: 29 outliers final: 14 residues processed: 97 average time/residue: 1.1086 time to fit residues: 114.9897 Evaluate side-chains 92 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 57 THR Chi-restraints excluded: chain B residue 66 SER 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 353 LEU Chi-restraints excluded: chain C residue 37 GLN 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 81 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 60 optimal weight: 0.5980 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.122844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.090005 restraints weight = 11498.417| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.58 r_work: 0.3109 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 8197 Z= 0.171 Angle : 0.656 17.265 11152 Z= 0.341 Chirality : 0.047 0.201 1237 Planarity : 0.004 0.034 1397 Dihedral : 8.788 74.265 1330 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.14 % Allowed : 16.55 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.27), residues: 984 helix: 1.30 (0.35), residues: 258 sheet: 0.86 (0.30), residues: 279 loop : -0.42 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 164 HIS 0.005 0.001 HIS A 116 PHE 0.031 0.002 PHE C 92 TYR 0.021 0.002 TYR B 43 ARG 0.008 0.001 ARG A 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00741 ( 8) link_NAG-ASN : angle 1.91374 ( 24) hydrogen bonds : bond 0.03152 ( 352) hydrogen bonds : angle 4.66242 ( 1026) SS BOND : bond 0.00304 ( 13) SS BOND : angle 3.65566 ( 26) covalent geometry : bond 0.00392 ( 8176) covalent geometry : angle 0.62701 (11102) *********************** 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 108 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 73 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 172 LYS cc_start: 0.8596 (tptt) cc_final: 0.8318 (tppp) REVERT: A 197 ARG cc_start: 0.9016 (mtp-110) cc_final: 0.8695 (mtp85) REVERT: A 258 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8250 (t70) REVERT: A 275 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8052 (mt0) REVERT: B 80 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7642 (tt) REVERT: B 197 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8327 (ttp80) REVERT: B 210 ASN cc_start: 0.7976 (OUTLIER) cc_final: 0.7598 (p0) REVERT: B 216 LYS cc_start: 0.8506 (mttp) cc_final: 0.8053 (pmmt) REVERT: C 197 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8262 (ttp-170) REVERT: C 210 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7799 (p0) REVERT: C 322 LYS cc_start: 0.8712 (ptmm) cc_final: 0.8407 (ptpp) outliers start: 35 outliers final: 15 residues processed: 97 average time/residue: 1.1077 time to fit residues: 114.9792 Evaluate side-chains 95 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER 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 57 THR Chi-restraints excluded: chain B residue 66 SER 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 69 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 48 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 89 optimal weight: 0.2980 chunk 30 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 73 optimal weight: 0.0970 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.125405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.091701 restraints weight = 11661.214| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.69 r_work: 0.3153 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8197 Z= 0.117 Angle : 0.593 13.879 11152 Z= 0.308 Chirality : 0.045 0.196 1237 Planarity : 0.004 0.033 1397 Dihedral : 8.371 70.957 1330 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.96 % Allowed : 17.73 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.27), residues: 984 helix: 1.79 (0.34), residues: 255 sheet: 0.80 (0.30), residues: 273 loop : -0.59 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 164 HIS 0.002 0.000 HIS B 306 PHE 0.021 0.001 PHE C 92 TYR 0.021 0.001 TYR B 43 ARG 0.007 0.000 ARG A 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00597 ( 8) link_NAG-ASN : angle 1.64359 ( 24) hydrogen bonds : bond 0.02716 ( 352) hydrogen bonds : angle 4.54308 ( 1026) SS BOND : bond 0.00365 ( 13) SS BOND : angle 3.50535 ( 26) covalent geometry : bond 0.00260 ( 8176) covalent geometry : angle 0.56459 (11102) *********************** 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 96 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LYS cc_start: 0.8609 (tptt) cc_final: 0.8298 (tppp) REVERT: A 197 ARG cc_start: 0.8994 (mtp-110) cc_final: 0.8669 (mtp85) REVERT: A 275 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8025 (mt0) REVERT: A 303 ASN cc_start: 0.8618 (m-40) cc_final: 0.8398 (t0) REVERT: B 80 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7658 (tt) REVERT: B 197 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8293 (ttp80) REVERT: B 210 ASN cc_start: 0.7943 (OUTLIER) cc_final: 0.7578 (p0) REVERT: B 216 LYS cc_start: 0.8452 (mttp) cc_final: 0.8003 (pmmt) REVERT: C 210 ASN cc_start: 0.8068 (OUTLIER) cc_final: 0.7829 (p0) REVERT: C 322 LYS cc_start: 0.8751 (ptmm) cc_final: 0.8450 (ptpp) outliers start: 25 outliers final: 11 residues processed: 91 average time/residue: 1.0667 time to fit residues: 104.1273 Evaluate side-chains 89 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 275 GLN 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 339 ILE Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 69 LEU 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 275 GLN Chi-restraints excluded: chain C residue 337 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 10 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.121658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.088804 restraints weight = 11457.338| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.59 r_work: 0.3077 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8197 Z= 0.209 Angle : 0.656 14.520 11152 Z= 0.343 Chirality : 0.047 0.222 1237 Planarity : 0.004 0.033 1397 Dihedral : 8.962 77.881 1330 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.48 % Allowed : 18.44 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.27), residues: 984 helix: 2.28 (0.34), residues: 237 sheet: 0.93 (0.30), residues: 279 loop : -0.46 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 47 HIS 0.003 0.001 HIS B 220 PHE 0.035 0.002 PHE C 92 TYR 0.016 0.002 TYR C 90 ARG 0.006 0.001 ARG A 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00586 ( 8) link_NAG-ASN : angle 1.69347 ( 24) hydrogen bonds : bond 0.03257 ( 352) hydrogen bonds : angle 4.68136 ( 1026) SS BOND : bond 0.00283 ( 13) SS BOND : angle 3.50590 ( 26) covalent geometry : bond 0.00486 ( 8176) covalent geometry : angle 0.63054 (11102) ********************** 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 98 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 THR cc_start: 0.8829 (m) cc_final: 0.8603 (p) REVERT: A 172 LYS cc_start: 0.8587 (tptt) cc_final: 0.8285 (tppp) REVERT: A 197 ARG cc_start: 0.9011 (mtp-110) cc_final: 0.8652 (mtp85) REVERT: A 275 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8207 (mm-40) REVERT: B 80 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7638 (tt) REVERT: B 159 CYS cc_start: 0.6662 (OUTLIER) cc_final: 0.5517 (m) REVERT: B 197 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8361 (ttp80) REVERT: B 210 ASN cc_start: 0.7935 (OUTLIER) cc_final: 0.7568 (p0) REVERT: B 216 LYS cc_start: 0.8516 (mttp) cc_final: 0.8101 (pmmt) REVERT: C 210 ASN cc_start: 0.8076 (OUTLIER) cc_final: 0.7784 (p0) REVERT: C 322 LYS cc_start: 0.8713 (ptmm) cc_final: 0.8402 (ptpp) outliers start: 21 outliers final: 11 residues processed: 91 average time/residue: 1.0945 time to fit residues: 106.7668 Evaluate side-chains 90 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 275 GLN Chi-restraints excluded: chain B residue 57 THR 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 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 275 GLN Chi-restraints excluded: chain C residue 337 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 80 optimal weight: 7.9990 chunk 22 optimal weight: 0.0570 chunk 77 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 67 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.124138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.090400 restraints weight = 11577.799| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.70 r_work: 0.3109 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8197 Z= 0.127 Angle : 0.615 12.821 11152 Z= 0.321 Chirality : 0.045 0.195 1237 Planarity : 0.004 0.039 1397 Dihedral : 8.751 74.433 1330 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.60 % Allowed : 18.79 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.27), residues: 984 helix: 1.79 (0.34), residues: 255 sheet: 0.85 (0.30), residues: 273 loop : -0.73 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 85 HIS 0.002 0.000 HIS C 116 PHE 0.026 0.002 PHE C 92 TYR 0.019 0.001 TYR A 90 ARG 0.007 0.000 ARG A 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00538 ( 8) link_NAG-ASN : angle 1.56363 ( 24) hydrogen bonds : bond 0.02827 ( 352) hydrogen bonds : angle 4.57906 ( 1026) SS BOND : bond 0.00426 ( 13) SS BOND : angle 3.56270 ( 26) covalent geometry : bond 0.00287 ( 8176) covalent geometry : angle 0.58697 (11102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7164.79 seconds wall clock time: 123 minutes 7.53 seconds (7387.53 seconds total)