Starting phenix.real_space_refine on Thu Feb 5 00:33:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ddw_46782/02_2026/9ddw_46782.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ddw_46782/02_2026/9ddw_46782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ddw_46782/02_2026/9ddw_46782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ddw_46782/02_2026/9ddw_46782.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ddw_46782/02_2026/9ddw_46782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ddw_46782/02_2026/9ddw_46782.map" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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: 6 Type Number sf(0) Gaussians P 9 5.49 5 S 36 5.16 5 C 4782 2.51 5 N 1236 2.21 5 O 1584 1.98 5 H 6039 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13686 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 4450 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 297} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 4450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 4450 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 297} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 4450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 4450 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 297} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {'ATP': 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: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {'ATP': 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: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {'ATP': 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: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Time building chain proxies: 2.26, per 1000 atoms: 0.17 Number of scatterers: 13686 At special positions: 0 Unit cell: (87.48, 90.072, 117.288, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 9 15.00 O 1584 8.00 N 1236 7.00 C 4782 6.00 H 6039 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 125 " - pdb=" SG CYS A 176 " distance=2.03 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 170 " distance=2.03 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 270 " - pdb=" SG CYS A 279 " distance=2.03 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS B 226 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 270 " - pdb=" SG CYS B 279 " distance=2.03 Simple disulfide: pdb=" SG CYS C 125 " - pdb=" SG CYS C 176 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 170 " distance=2.03 Simple disulfide: pdb=" SG CYS C 226 " - pdb=" SG CYS C 236 " distance=2.03 Simple disulfide: pdb=" SG CYS C 270 " - pdb=" SG CYS C 279 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 133 " " NAG A 502 " - " ASN A 194 " " NAG B 501 " - " ASN B 133 " " NAG B 502 " - " ASN B 194 " " NAG C 501 " - " ASN C 133 " " NAG C 502 " - " ASN C 194 " Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 296.9 milliseconds 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1716 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 9 sheets defined 25.0% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 43 through 56 Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 191 through 194 Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 337 through 355 Processing helix chain 'B' and resid 44 through 56 Processing helix chain 'B' and resid 94 through 98 Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 241 through 248 Processing helix chain 'B' and resid 251 through 258 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 337 through 355 Processing helix chain 'C' and resid 44 through 56 Processing helix chain 'C' and resid 94 through 98 Processing helix chain 'C' and resid 138 through 142 Processing helix chain 'C' and resid 178 through 183 Processing helix chain 'C' and resid 191 through 194 Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 241 through 248 Processing helix chain 'C' and resid 251 through 258 Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 337 through 355 Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 68 through 72 current: chain 'A' and resid 107 through 126 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 107 through 126 current: chain 'A' and resid 168 through 176 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 168 through 176 current: chain 'A' and resid 281 through 287 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 281 through 287 current: chain 'A' and resid 312 through 336 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 75 through 83 Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 88 Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 68 through 72 current: chain 'B' and resid 107 through 126 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 107 through 126 current: chain 'B' and resid 168 through 176 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 168 through 176 current: chain 'B' and resid 281 through 287 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 281 through 287 current: chain 'B' and resid 312 through 336 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 75 through 83 Processing sheet with id=AA6, first strand: chain 'B' and resid 86 through 88 Processing sheet with id=AA7, first strand: chain 'C' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 68 through 72 current: chain 'C' and resid 107 through 126 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 107 through 126 current: chain 'C' and resid 168 through 176 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 168 through 176 current: chain 'C' and resid 281 through 287 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 281 through 287 current: chain 'C' and resid 312 through 336 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 75 through 83 Processing sheet with id=AA9, first strand: chain 'C' and resid 86 through 88 181 hydrogen bonds defined for protein. 435 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: 2.70 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.88: 1193 0.88 - 1.11: 4723 1.11 - 1.35: 2469 1.35 - 1.59: 5277 1.59 - 1.82: 57 Bond restraints: 13719 Sorted by residual: bond pdb=" NZ LYS A 168 " pdb=" HZ3 LYS A 168 " ideal model delta sigma weight residual 0.890 1.132 -0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" NZ LYS C 168 " pdb=" HZ3 LYS C 168 " ideal model delta sigma weight residual 0.890 1.131 -0.241 2.00e-02 2.50e+03 1.46e+02 bond pdb=" NZ LYS B 168 " pdb=" HZ3 LYS B 168 " ideal model delta sigma weight residual 0.890 1.130 -0.240 2.00e-02 2.50e+03 1.45e+02 bond pdb=" CE LYS B 168 " pdb=" HE3 LYS B 168 " ideal model delta sigma weight residual 0.970 0.739 0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" CE LYS C 168 " pdb=" HE3 LYS C 168 " ideal model delta sigma weight residual 0.970 0.740 0.230 2.00e-02 2.50e+03 1.32e+02 ... (remaining 13714 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.78: 22544 7.78 - 15.56: 1605 15.56 - 23.34: 85 23.34 - 31.11: 3 31.11 - 38.89: 6 Bond angle restraints: 24243 Sorted by residual: angle pdb=" PB ATP A 500 " pdb=" O3B ATP A 500 " pdb=" PG ATP A 500 " ideal model delta sigma weight residual 139.87 122.12 17.75 1.00e+00 1.00e+00 3.15e+02 angle pdb=" PB ATP B 500 " pdb=" O3B ATP B 500 " pdb=" PG ATP B 500 " ideal model delta sigma weight residual 139.87 122.12 17.75 1.00e+00 1.00e+00 3.15e+02 angle pdb=" PB ATP C 500 " pdb=" O3B ATP C 500 " pdb=" PG ATP C 500 " ideal model delta sigma weight residual 139.87 122.16 17.71 1.00e+00 1.00e+00 3.14e+02 angle pdb=" C LYS B 291 " pdb=" CA LYS B 291 " pdb=" HA LYS B 291 " ideal model delta sigma weight residual 109.00 70.11 38.89 3.00e+00 1.11e-01 1.68e+02 angle pdb=" C LYS A 291 " pdb=" CA LYS A 291 " pdb=" HA LYS A 291 " ideal model delta sigma weight residual 109.00 70.12 38.88 3.00e+00 1.11e-01 1.68e+02 ... (remaining 24238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.99: 5783 13.99 - 27.97: 637 27.97 - 41.96: 216 41.96 - 55.94: 147 55.94 - 69.93: 21 Dihedral angle restraints: 6804 sinusoidal: 3630 harmonic: 3174 Sorted by residual: dihedral pdb=" CB CYS C 270 " pdb=" SG CYS C 270 " pdb=" SG CYS C 279 " pdb=" CB CYS C 279 " ideal model delta sinusoidal sigma weight residual 93.00 56.30 36.70 1 1.00e+01 1.00e-02 1.90e+01 dihedral pdb=" CB CYS B 270 " pdb=" SG CYS B 270 " pdb=" SG CYS B 279 " pdb=" CB CYS B 279 " ideal model delta sinusoidal sigma weight residual 93.00 56.32 36.68 1 1.00e+01 1.00e-02 1.90e+01 dihedral pdb=" CB CYS A 270 " pdb=" SG CYS A 270 " pdb=" SG CYS A 279 " pdb=" CB CYS A 279 " ideal model delta sinusoidal sigma weight residual 93.00 56.38 36.62 1 1.00e+01 1.00e-02 1.90e+01 ... (remaining 6801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1015 0.080 - 0.161: 164 0.161 - 0.241: 3 0.241 - 0.321: 0 0.321 - 0.401: 3 Chirality restraints: 1185 Sorted by residual: chirality pdb=" CA LYS A 291 " pdb=" N LYS A 291 " pdb=" C LYS A 291 " pdb=" CB LYS A 291 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CA LYS C 291 " pdb=" N LYS C 291 " pdb=" C LYS C 291 " pdb=" CB LYS C 291 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CA LYS B 291 " pdb=" N LYS B 291 " pdb=" C LYS B 291 " pdb=" CB LYS B 291 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.00e+00 ... (remaining 1182 not shown) Planarity restraints: 2064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 336 " 0.018 2.00e-02 2.50e+03 7.67e-02 1.76e+02 pdb=" CG PHE C 336 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE C 336 " 0.060 2.00e-02 2.50e+03 pdb=" CD2 PHE C 336 " 0.054 2.00e-02 2.50e+03 pdb=" CE1 PHE C 336 " 0.085 2.00e-02 2.50e+03 pdb=" CE2 PHE C 336 " 0.080 2.00e-02 2.50e+03 pdb=" CZ PHE C 336 " 0.095 2.00e-02 2.50e+03 pdb=" HD1 PHE C 336 " -0.103 2.00e-02 2.50e+03 pdb=" HD2 PHE C 336 " -0.117 2.00e-02 2.50e+03 pdb=" HE1 PHE C 336 " -0.071 2.00e-02 2.50e+03 pdb=" HE2 PHE C 336 " -0.082 2.00e-02 2.50e+03 pdb=" HZ PHE C 336 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 336 " 0.018 2.00e-02 2.50e+03 7.65e-02 1.76e+02 pdb=" CG PHE A 336 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 336 " 0.060 2.00e-02 2.50e+03 pdb=" CD2 PHE A 336 " 0.054 2.00e-02 2.50e+03 pdb=" CE1 PHE A 336 " 0.085 2.00e-02 2.50e+03 pdb=" CE2 PHE A 336 " 0.080 2.00e-02 2.50e+03 pdb=" CZ PHE A 336 " 0.095 2.00e-02 2.50e+03 pdb=" HD1 PHE A 336 " -0.103 2.00e-02 2.50e+03 pdb=" HD2 PHE A 336 " -0.116 2.00e-02 2.50e+03 pdb=" HE1 PHE A 336 " -0.070 2.00e-02 2.50e+03 pdb=" HE2 PHE A 336 " -0.082 2.00e-02 2.50e+03 pdb=" HZ PHE A 336 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 336 " -0.018 2.00e-02 2.50e+03 7.63e-02 1.75e+02 pdb=" CG PHE B 336 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE B 336 " -0.059 2.00e-02 2.50e+03 pdb=" CD2 PHE B 336 " -0.053 2.00e-02 2.50e+03 pdb=" CE1 PHE B 336 " -0.085 2.00e-02 2.50e+03 pdb=" CE2 PHE B 336 " -0.079 2.00e-02 2.50e+03 pdb=" CZ PHE B 336 " -0.095 2.00e-02 2.50e+03 pdb=" HD1 PHE B 336 " 0.103 2.00e-02 2.50e+03 pdb=" HD2 PHE B 336 " 0.116 2.00e-02 2.50e+03 pdb=" HE1 PHE B 336 " 0.070 2.00e-02 2.50e+03 pdb=" HE2 PHE B 336 " 0.082 2.00e-02 2.50e+03 pdb=" HZ PHE B 336 " 0.060 2.00e-02 2.50e+03 ... (remaining 2061 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 751 2.17 - 2.78: 24061 2.78 - 3.39: 34896 3.39 - 3.99: 51209 3.99 - 4.60: 76592 Nonbonded interactions: 187509 Sorted by model distance: nonbonded pdb=" H LYS A 291 " pdb=" HA LYS A 291 " model vdw 1.565 1.816 nonbonded pdb=" H LYS C 291 " pdb=" HA LYS C 291 " model vdw 1.565 1.816 nonbonded pdb=" H LYS B 291 " pdb=" HA LYS B 291 " model vdw 1.565 1.816 nonbonded pdb=" O GLY A 84 " pdb=" HH TYR A 98 " model vdw 1.570 2.450 nonbonded pdb=" O GLY B 84 " pdb=" HH TYR B 98 " model vdw 1.572 2.450 ... (remaining 187504 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 43 through 355 or resid 501)) selection = (chain 'B' and (resid 43 through 355 or resid 502)) selection = (chain 'C' and (resid 43 through 355 or resid 502)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.390 Find NCS groups from input model: 0.150 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: 0.010 Load rotamer database and sin/cos tables:5.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 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 : 0.007 0.089 7701 Z= 0.431 Angle : 0.968 17.751 10503 Z= 0.654 Chirality : 0.056 0.401 1185 Planarity : 0.005 0.049 1299 Dihedral : 13.819 69.926 2907 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.26), residues: 933 helix: -0.72 (0.40), residues: 201 sheet: 0.01 (0.24), residues: 345 loop : -0.71 (0.28), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 286 TYR 0.014 0.002 TYR A 98 PHE 0.049 0.003 PHE B 208 TRP 0.015 0.002 TRP C 268 HIS 0.004 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00729 ( 7680) covalent geometry : angle 0.95991 (10455) SS BOND : bond 0.00298 ( 15) SS BOND : angle 1.10957 ( 30) hydrogen bonds : bond 0.22152 ( 181) hydrogen bonds : angle 6.29462 ( 435) link_NAG-ASN : bond 0.00201 ( 6) link_NAG-ASN : angle 3.12921 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ILE cc_start: 0.8624 (mm) cc_final: 0.8416 (mp) REVERT: A 159 CYS cc_start: 0.5833 (t) cc_final: 0.5547 (t) REVERT: A 284 SER cc_start: 0.8045 (m) cc_final: 0.7752 (m) REVERT: B 152 ASN cc_start: 0.7762 (m110) cc_final: 0.7424 (m-40) REVERT: B 159 CYS cc_start: 0.5419 (t) cc_final: 0.5135 (t) REVERT: B 289 ASP cc_start: 0.7483 (p0) cc_final: 0.7266 (p0) REVERT: C 56 PHE cc_start: 0.6835 (t80) cc_final: 0.6418 (t80) REVERT: C 98 TYR cc_start: 0.8032 (p90) cc_final: 0.7812 (p90) REVERT: C 156 THR cc_start: 0.8349 (p) cc_final: 0.8081 (t) REVERT: C 254 GLU cc_start: 0.6885 (tm-30) cc_final: 0.6645 (tm-30) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.9779 time to fit residues: 200.2941 Evaluate side-chains 173 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN B 122 GLN C 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.128252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.109383 restraints weight = 28728.034| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.31 r_work: 0.3468 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 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 : 0.005 0.051 7701 Z= 0.205 Angle : 0.575 4.543 10503 Z= 0.312 Chirality : 0.052 0.383 1185 Planarity : 0.005 0.045 1299 Dihedral : 10.562 85.259 1242 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.87 % Allowed : 8.24 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.26), residues: 933 helix: -0.83 (0.35), residues: 240 sheet: 0.25 (0.26), residues: 345 loop : -0.68 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 158 TYR 0.017 0.002 TYR C 98 PHE 0.015 0.002 PHE C 336 TRP 0.012 0.001 TRP B 268 HIS 0.003 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 7680) covalent geometry : angle 0.56642 (10455) SS BOND : bond 0.00499 ( 15) SS BOND : angle 1.29099 ( 30) hydrogen bonds : bond 0.04577 ( 181) hydrogen bonds : angle 4.28909 ( 435) link_NAG-ASN : bond 0.00478 ( 6) link_NAG-ASN : angle 1.94876 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 224 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8417 (mt-10) REVERT: B 159 CYS cc_start: 0.6669 (t) cc_final: 0.6319 (t) REVERT: B 274 LEU cc_start: 0.8280 (mt) cc_final: 0.8075 (mt) REVERT: C 254 GLU cc_start: 0.7416 (tm-30) cc_final: 0.7213 (tm-30) REVERT: C 258 LYS cc_start: 0.8490 (mmmm) cc_final: 0.8218 (mmmm) outliers start: 7 outliers final: 3 residues processed: 225 average time/residue: 1.0490 time to fit residues: 248.4532 Evaluate side-chains 212 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 209 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain C residue 350 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 81 optimal weight: 0.3980 chunk 82 optimal weight: 0.8980 chunk 78 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN B 280 ASN C 280 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.125722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.106827 restraints weight = 28716.036| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.30 r_work: 0.3425 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 7701 Z= 0.197 Angle : 0.520 4.604 10503 Z= 0.280 Chirality : 0.051 0.409 1185 Planarity : 0.005 0.050 1299 Dihedral : 9.821 83.155 1242 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.00 % Allowed : 13.11 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.27), residues: 933 helix: -0.44 (0.37), residues: 240 sheet: 0.21 (0.26), residues: 342 loop : -0.63 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 158 TYR 0.011 0.001 TYR A 222 PHE 0.012 0.001 PHE C 210 TRP 0.009 0.001 TRP A 58 HIS 0.002 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 7680) covalent geometry : angle 0.51084 (10455) SS BOND : bond 0.00442 ( 15) SS BOND : angle 1.15491 ( 30) hydrogen bonds : bond 0.04338 ( 181) hydrogen bonds : angle 4.05582 ( 435) link_NAG-ASN : bond 0.00465 ( 6) link_NAG-ASN : angle 2.05157 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 219 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 159 CYS cc_start: 0.6708 (t) cc_final: 0.6382 (t) REVERT: B 191 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.7985 (mtp) REVERT: B 235 TYR cc_start: 0.8475 (m-80) cc_final: 0.8218 (m-80) REVERT: C 254 GLU cc_start: 0.7485 (tm-30) cc_final: 0.7260 (tm-30) REVERT: C 258 LYS cc_start: 0.8587 (mmmm) cc_final: 0.8282 (mmmm) outliers start: 8 outliers final: 2 residues processed: 221 average time/residue: 1.1109 time to fit residues: 258.0344 Evaluate side-chains 219 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 216 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 209 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 152 ASN B 280 ASN C 280 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.124415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.105083 restraints weight = 28340.089| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.30 r_work: 0.3398 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 7701 Z= 0.288 Angle : 0.549 4.855 10503 Z= 0.298 Chirality : 0.053 0.395 1185 Planarity : 0.005 0.051 1299 Dihedral : 10.219 82.986 1242 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.87 % Allowed : 15.23 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.27), residues: 933 helix: 0.45 (0.41), residues: 192 sheet: 0.21 (0.26), residues: 342 loop : -0.68 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 218 TYR 0.018 0.002 TYR B 98 PHE 0.015 0.002 PHE C 210 TRP 0.010 0.001 TRP B 268 HIS 0.003 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00706 ( 7680) covalent geometry : angle 0.54088 (10455) SS BOND : bond 0.00547 ( 15) SS BOND : angle 1.20332 ( 30) hydrogen bonds : bond 0.04414 ( 181) hydrogen bonds : angle 4.14685 ( 435) link_NAG-ASN : bond 0.00407 ( 6) link_NAG-ASN : angle 1.95841 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 219 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8428 (mtt180) REVERT: B 158 ARG cc_start: 0.7932 (mtm180) cc_final: 0.7719 (mtm180) REVERT: B 159 CYS cc_start: 0.6735 (t) cc_final: 0.6408 (t) REVERT: B 171 GLU cc_start: 0.7884 (tt0) cc_final: 0.7585 (tt0) REVERT: C 254 GLU cc_start: 0.7531 (tm-30) cc_final: 0.7305 (tm-30) REVERT: C 258 LYS cc_start: 0.8638 (mmmm) cc_final: 0.8324 (mmmm) outliers start: 7 outliers final: 2 residues processed: 221 average time/residue: 1.1897 time to fit residues: 275.9787 Evaluate side-chains 213 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 210 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 343 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 10 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 75 optimal weight: 0.0040 chunk 0 optimal weight: 8.9990 chunk 15 optimal weight: 0.1980 chunk 29 optimal weight: 0.9980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 152 ASN B 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.124756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.105738 restraints weight = 28698.917| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.30 r_work: 0.3410 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7701 Z= 0.172 Angle : 0.487 4.506 10503 Z= 0.264 Chirality : 0.051 0.389 1185 Planarity : 0.005 0.057 1299 Dihedral : 9.755 78.104 1242 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.37 % Allowed : 16.73 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.27), residues: 933 helix: 0.66 (0.42), residues: 192 sheet: 0.16 (0.26), residues: 336 loop : -0.51 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 315 TYR 0.016 0.001 TYR B 98 PHE 0.017 0.001 PHE C 336 TRP 0.008 0.001 TRP A 58 HIS 0.002 0.000 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 7680) covalent geometry : angle 0.47858 (10455) SS BOND : bond 0.00400 ( 15) SS BOND : angle 0.93873 ( 30) hydrogen bonds : bond 0.03770 ( 181) hydrogen bonds : angle 3.98847 ( 435) link_NAG-ASN : bond 0.00395 ( 6) link_NAG-ASN : angle 1.90987 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 217 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8402 (mtt180) REVERT: A 225 ARG cc_start: 0.8667 (ptm-80) cc_final: 0.8426 (ptt-90) REVERT: A 250 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7953 (mm-30) REVERT: B 159 CYS cc_start: 0.6624 (t) cc_final: 0.6297 (t) REVERT: C 254 GLU cc_start: 0.7519 (tm-30) cc_final: 0.7318 (tm-30) REVERT: C 258 LYS cc_start: 0.8607 (mmmm) cc_final: 0.8302 (mmmm) outliers start: 11 outliers final: 5 residues processed: 220 average time/residue: 1.1137 time to fit residues: 257.4207 Evaluate side-chains 222 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 216 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 350 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 33 optimal weight: 0.0060 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 80 optimal weight: 0.3980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 152 ASN B 280 ASN ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.124532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.105627 restraints weight = 28821.425| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.30 r_work: 0.3406 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7701 Z= 0.172 Angle : 0.480 4.531 10503 Z= 0.261 Chirality : 0.051 0.389 1185 Planarity : 0.005 0.057 1299 Dihedral : 9.629 76.970 1242 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.50 % Allowed : 16.85 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.27), residues: 933 helix: 0.76 (0.42), residues: 192 sheet: 0.13 (0.27), residues: 336 loop : -0.47 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 158 TYR 0.015 0.001 TYR B 98 PHE 0.023 0.001 PHE C 336 TRP 0.008 0.001 TRP A 58 HIS 0.002 0.000 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 7680) covalent geometry : angle 0.47371 (10455) SS BOND : bond 0.00387 ( 15) SS BOND : angle 0.91321 ( 30) hydrogen bonds : bond 0.03652 ( 181) hydrogen bonds : angle 3.93816 ( 435) link_NAG-ASN : bond 0.00386 ( 6) link_NAG-ASN : angle 1.70905 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 220 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8416 (mtt180) REVERT: A 225 ARG cc_start: 0.8679 (ptm-80) cc_final: 0.8362 (ptt-90) REVERT: A 250 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7966 (mm-30) REVERT: B 159 CYS cc_start: 0.6652 (t) cc_final: 0.6316 (t) REVERT: B 324 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.7684 (ttm-80) REVERT: C 247 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8404 (mptm) REVERT: C 258 LYS cc_start: 0.8626 (mmmm) cc_final: 0.8320 (mmmm) outliers start: 12 outliers final: 5 residues processed: 225 average time/residue: 1.1964 time to fit residues: 282.1843 Evaluate side-chains 225 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 217 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 247 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 13 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 2 optimal weight: 0.0170 chunk 43 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 78 optimal weight: 0.1980 chunk 87 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 152 ASN B 280 ASN ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.124765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.106088 restraints weight = 28684.311| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.28 r_work: 0.3414 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 7701 Z= 0.155 Angle : 0.471 4.461 10503 Z= 0.256 Chirality : 0.050 0.389 1185 Planarity : 0.005 0.060 1299 Dihedral : 9.461 74.278 1242 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.25 % Allowed : 17.60 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.27), residues: 933 helix: 0.87 (0.42), residues: 192 sheet: 0.11 (0.27), residues: 336 loop : -0.43 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 155 TYR 0.014 0.001 TYR B 98 PHE 0.019 0.001 PHE C 336 TRP 0.008 0.001 TRP A 58 HIS 0.002 0.000 HIS B 204 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 7680) covalent geometry : angle 0.46549 (10455) SS BOND : bond 0.00351 ( 15) SS BOND : angle 0.84725 ( 30) hydrogen bonds : bond 0.03498 ( 181) hydrogen bonds : angle 3.92278 ( 435) link_NAG-ASN : bond 0.00389 ( 6) link_NAG-ASN : angle 1.62527 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 223 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 ARG cc_start: 0.8679 (ptm-80) cc_final: 0.8363 (ptt-90) REVERT: A 250 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7955 (mm-30) REVERT: B 159 CYS cc_start: 0.6659 (t) cc_final: 0.6324 (t) REVERT: B 324 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.7685 (ttm-80) REVERT: B 350 THR cc_start: 0.7942 (m) cc_final: 0.7727 (p) REVERT: C 247 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8400 (mptm) REVERT: C 258 LYS cc_start: 0.8605 (mmmm) cc_final: 0.8314 (mmmm) outliers start: 10 outliers final: 5 residues processed: 227 average time/residue: 1.0436 time to fit residues: 248.8349 Evaluate side-chains 228 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 221 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain C residue 247 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 59 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 81 optimal weight: 0.0170 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN B 280 ASN ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.124441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.105616 restraints weight = 28561.564| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.28 r_work: 0.3406 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 7701 Z= 0.188 Angle : 0.485 4.571 10503 Z= 0.264 Chirality : 0.051 0.390 1185 Planarity : 0.005 0.059 1299 Dihedral : 9.536 75.248 1242 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.37 % Allowed : 17.35 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.27), residues: 933 helix: 0.86 (0.42), residues: 192 sheet: 0.08 (0.27), residues: 336 loop : -0.45 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 315 TYR 0.013 0.001 TYR B 98 PHE 0.023 0.001 PHE C 336 TRP 0.010 0.001 TRP B 58 HIS 0.002 0.000 HIS B 204 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 7680) covalent geometry : angle 0.47939 (10455) SS BOND : bond 0.00405 ( 15) SS BOND : angle 0.92767 ( 30) hydrogen bonds : bond 0.03648 ( 181) hydrogen bonds : angle 3.95653 ( 435) link_NAG-ASN : bond 0.00359 ( 6) link_NAG-ASN : angle 1.61314 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 221 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 ARG cc_start: 0.8696 (ptm-80) cc_final: 0.8381 (ptt-90) REVERT: A 250 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7962 (mm-30) REVERT: B 159 CYS cc_start: 0.6643 (t) cc_final: 0.6310 (t) REVERT: B 324 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.7689 (ttm-80) REVERT: B 350 THR cc_start: 0.7933 (OUTLIER) cc_final: 0.7722 (p) REVERT: C 247 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8415 (mptm) REVERT: C 258 LYS cc_start: 0.8618 (mmmm) cc_final: 0.8338 (mmmm) outliers start: 11 outliers final: 4 residues processed: 226 average time/residue: 1.0634 time to fit residues: 252.8267 Evaluate side-chains 226 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 219 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 247 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 55 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 35 optimal weight: 0.3980 chunk 58 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 82 optimal weight: 0.2980 chunk 76 optimal weight: 0.9980 chunk 52 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 152 ASN B 280 ASN ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.124125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.105432 restraints weight = 28829.806| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.28 r_work: 0.3404 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 7701 Z= 0.191 Angle : 0.486 4.587 10503 Z= 0.264 Chirality : 0.051 0.391 1185 Planarity : 0.005 0.068 1299 Dihedral : 9.602 77.990 1242 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.12 % Allowed : 18.35 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.27), residues: 933 helix: 0.87 (0.42), residues: 192 sheet: 0.08 (0.27), residues: 336 loop : -0.44 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 315 TYR 0.013 0.001 TYR B 98 PHE 0.019 0.001 PHE C 336 TRP 0.012 0.001 TRP B 58 HIS 0.002 0.000 HIS B 204 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 7680) covalent geometry : angle 0.48013 (10455) SS BOND : bond 0.00417 ( 15) SS BOND : angle 0.89043 ( 30) hydrogen bonds : bond 0.03622 ( 181) hydrogen bonds : angle 3.95295 ( 435) link_NAG-ASN : bond 0.00344 ( 6) link_NAG-ASN : angle 1.61825 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 216 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7994 (mm-30) REVERT: A 293 VAL cc_start: 0.8286 (t) cc_final: 0.8079 (m) REVERT: B 159 CYS cc_start: 0.6665 (t) cc_final: 0.6330 (t) REVERT: B 324 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.7673 (ttm-80) REVERT: B 350 THR cc_start: 0.7941 (OUTLIER) cc_final: 0.7729 (p) REVERT: C 247 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8411 (mptm) REVERT: C 258 LYS cc_start: 0.8620 (mmmm) cc_final: 0.8354 (mmmm) outliers start: 9 outliers final: 4 residues processed: 220 average time/residue: 1.1349 time to fit residues: 262.2785 Evaluate side-chains 223 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 216 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 247 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 82 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 62 optimal weight: 10.0000 chunk 10 optimal weight: 0.0570 chunk 59 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 chunk 14 optimal weight: 0.3980 chunk 90 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 152 ASN B 280 ASN ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.124886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.106189 restraints weight = 28531.078| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.28 r_work: 0.3414 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7701 Z= 0.135 Angle : 0.464 4.367 10503 Z= 0.253 Chirality : 0.050 0.389 1185 Planarity : 0.005 0.063 1299 Dihedral : 9.378 74.698 1242 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.75 % Allowed : 19.23 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.28), residues: 933 helix: 0.99 (0.43), residues: 192 sheet: 0.10 (0.27), residues: 336 loop : -0.36 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 225 TYR 0.015 0.001 TYR B 98 PHE 0.019 0.001 PHE C 336 TRP 0.010 0.001 TRP B 58 HIS 0.001 0.000 HIS B 204 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 7680) covalent geometry : angle 0.45897 (10455) SS BOND : bond 0.00334 ( 15) SS BOND : angle 0.78545 ( 30) hydrogen bonds : bond 0.03305 ( 181) hydrogen bonds : angle 3.87522 ( 435) link_NAG-ASN : bond 0.00378 ( 6) link_NAG-ASN : angle 1.50831 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 215 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7951 (mm-30) REVERT: B 159 CYS cc_start: 0.6648 (t) cc_final: 0.6312 (t) REVERT: C 247 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8407 (mptm) REVERT: C 258 LYS cc_start: 0.8599 (mmmm) cc_final: 0.8331 (mmmm) outliers start: 6 outliers final: 4 residues processed: 218 average time/residue: 1.1195 time to fit residues: 256.3187 Evaluate side-chains 219 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 214 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain C residue 247 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 61 optimal weight: 0.5980 chunk 46 optimal weight: 0.4980 chunk 60 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 0.0980 chunk 52 optimal weight: 0.8980 chunk 49 optimal weight: 0.0670 chunk 47 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN A 280 ASN ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN B 280 ASN ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.124427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.106139 restraints weight = 28497.150| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.25 r_work: 0.3418 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7701 Z= 0.133 Angle : 0.460 4.329 10503 Z= 0.251 Chirality : 0.050 0.391 1185 Planarity : 0.005 0.060 1299 Dihedral : 9.250 72.370 1242 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.50 % Allowed : 19.60 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.28), residues: 933 helix: 0.99 (0.42), residues: 192 sheet: 0.11 (0.27), residues: 336 loop : -0.34 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 315 TYR 0.015 0.001 TYR B 98 PHE 0.018 0.001 PHE C 336 TRP 0.009 0.001 TRP B 58 HIS 0.001 0.000 HIS B 204 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 7680) covalent geometry : angle 0.45517 (10455) SS BOND : bond 0.00322 ( 15) SS BOND : angle 0.77120 ( 30) hydrogen bonds : bond 0.03266 ( 181) hydrogen bonds : angle 3.85442 ( 435) link_NAG-ASN : bond 0.00368 ( 6) link_NAG-ASN : angle 1.43160 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6597.82 seconds wall clock time: 112 minutes 4.35 seconds (6724.35 seconds total)