Starting phenix.real_space_refine on Fri Sep 11 00:25:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6y3y_10676/09_2026/6y3y_10676.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y3y_10676/09_2026/6y3y_10676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6y3y_10676/09_2026/6y3y_10676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y3y_10676/09_2026/6y3y_10676.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6y3y_10676/09_2026/6y3y_10676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y3y_10676/09_2026/6y3y_10676.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6y3y_10676/09_2026/6y3y_10676.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6y3y_10676/09_2026/6y3y_10676.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 3778 2.51 5 N 886 2.21 5 O 1164 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5854 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2707 Classifications: {'peptide': 332} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 316} Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: B, G, H, I, J Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" C1 NAG A 406 " occ=0.81 ... (12 atoms not shown) pdb=" O7 NAG A 406 " occ=0.81 residue: pdb=" C1 NAG A 407 " occ=0.44 ... (12 atoms not shown) pdb=" O7 NAG A 407 " occ=0.44 residue: pdb=" C1 NAG B 406 " occ=0.81 ... (12 atoms not shown) pdb=" O7 NAG B 406 " occ=0.81 residue: pdb=" C1 NAG B 407 " occ=0.44 ... (12 atoms not shown) pdb=" O7 NAG B 407 " occ=0.44 Time building chain proxies: 1.99, per 1000 atoms: 0.34 Number of scatterers: 5854 At special positions: 0 Unit cell: (105.455, 73.255, 88.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 1164 8.00 N 886 7.00 C 3778 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 38 " - pdb=" SG CYS A 59 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 154 " distance=2.02 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 188 " - pdb=" SG CYS A 219 " distance=2.03 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 282 " distance=2.03 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 341 " distance=2.03 Simple disulfide: pdb=" SG CYS B 38 " - pdb=" SG CYS B 59 " distance=2.03 Simple disulfide: pdb=" SG CYS B 107 " - pdb=" SG CYS B 154 " distance=2.02 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 188 " - pdb=" SG CYS B 219 " distance=2.03 Simple disulfide: pdb=" SG CYS B 277 " - pdb=" SG CYS B 282 " distance=2.03 Simple disulfide: pdb=" SG CYS B 317 " - pdb=" SG CYS B 341 " 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 ALPHA1-3 " BMA C 3 " - " MAN C 4 " " BMA D 3 " - " MAN D 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " ALPHA1-6 " BMA D 3 " - " MAN D 5 " " BMA H 3 " - " MAN H 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 405 " - " ASN A 110 " " NAG A 406 " - " ASN A 145 " " NAG A 407 " - " ASN A 193 " " NAG B 405 " - " ASN B 110 " " NAG B 406 " - " ASN B 145 " " NAG B 407 " - " ASN B 193 " " NAG C 1 " - " ASN A 83 " " NAG D 1 " - " ASN A 286 " " NAG E 1 " - " ASN A 314 " " NAG F 1 " - " ASN A 328 " " NAG G 1 " - " ASN B 83 " " NAG H 1 " - " ASN B 286 " " NAG I 1 " - " ASN B 314 " " NAG J 1 " - " ASN B 328 " Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 451.6 milliseconds 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1260 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 11 sheets defined 17.2% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 33 through 37 removed outlier: 3.738A pdb=" N ASP A 37 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 44 removed outlier: 3.518A pdb=" N LEU A 44 " --> pdb=" O ILE A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 78 Processing helix chain 'A' and resid 113 through 132 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 301 through 309 Processing helix chain 'A' and resid 310 through 313 removed outlier: 3.689A pdb=" N TYR A 313 " --> pdb=" O GLY A 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 310 through 313' Processing helix chain 'B' and resid 33 through 37 removed outlier: 3.737A pdb=" N ASP B 37 " --> pdb=" O SER B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 44 removed outlier: 3.517A pdb=" N LEU B 44 " --> pdb=" O ILE B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 78 Processing helix chain 'B' and resid 113 through 132 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 301 through 309 Processing helix chain 'B' and resid 310 through 313 removed outlier: 3.689A pdb=" N TYR B 313 " --> pdb=" O GLY B 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 310 through 313' Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 removed outlier: 8.627A pdb=" N SER A 65 " --> pdb=" O TRP A 28 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU A 30 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE A 29 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE A 91 " --> pdb=" O GLN A 257 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N VAL A 259 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE A 93 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 87 removed outlier: 8.426A pdb=" N LYS A 243 " --> pdb=" O PRO A 186 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A 184 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 165 through 168 Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 176 removed outlier: 3.733A pdb=" N VAL A 173 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 196 through 197 removed outlier: 4.276A pdb=" N VAL A 206 " --> pdb=" O GLY B 208 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY B 208 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY A 208 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL B 206 " --> pdb=" O GLY A 208 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 317 through 318 Processing sheet with id=AA7, first strand: chain 'B' and resid 64 through 65 removed outlier: 8.627A pdb=" N SER B 65 " --> pdb=" O TRP B 28 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU B 30 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE B 29 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE B 91 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N VAL B 259 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE B 93 " --> pdb=" O VAL B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87 removed outlier: 8.426A pdb=" N LYS B 243 " --> pdb=" O PRO B 186 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU B 184 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 165 through 168 Processing sheet with id=AB1, first strand: chain 'B' and resid 173 through 176 removed outlier: 3.732A pdb=" N VAL B 173 " --> pdb=" O VAL B 231 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 317 through 318 120 hydrogen bonds defined for protein. 312 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.90 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1682 1.34 - 1.46: 1772 1.46 - 1.58: 2546 1.58 - 1.70: 0 1.70 - 1.82: 28 Bond restraints: 6028 Sorted by residual: bond pdb=" C PHE A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 1.334 1.503 -0.169 2.34e-02 1.83e+03 5.20e+01 bond pdb=" C PHE B 108 " pdb=" N PRO B 109 " ideal model delta sigma weight residual 1.334 1.503 -0.169 2.34e-02 1.83e+03 5.20e+01 bond pdb=" C1 NAG B 405 " pdb=" O5 NAG B 405 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.50e+00 bond pdb=" C1 NAG A 405 " pdb=" O5 NAG A 405 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.44e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.42e+00 ... (remaining 6023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 7885 2.41 - 4.81: 252 4.81 - 7.22: 51 7.22 - 9.63: 6 9.63 - 12.04: 4 Bond angle restraints: 8198 Sorted by residual: angle pdb=" C PHE A 108 " pdb=" N PRO A 109 " pdb=" CA PRO A 109 " ideal model delta sigma weight residual 119.84 131.88 -12.04 1.25e+00 6.40e-01 9.27e+01 angle pdb=" C PHE B 108 " pdb=" N PRO B 109 " pdb=" CA PRO B 109 " ideal model delta sigma weight residual 119.84 131.84 -12.00 1.25e+00 6.40e-01 9.22e+01 angle pdb=" CA PHE A 108 " pdb=" C PHE A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 118.56 125.78 -7.22 1.31e+00 5.83e-01 3.03e+01 angle pdb=" CA PHE B 108 " pdb=" C PHE B 108 " pdb=" N PRO B 109 " ideal model delta sigma weight residual 118.56 125.74 -7.18 1.31e+00 5.83e-01 3.00e+01 angle pdb=" CA PHE B 108 " pdb=" C PHE B 108 " pdb=" O PHE B 108 " ideal model delta sigma weight residual 119.22 114.87 4.35 1.02e+00 9.61e-01 1.82e+01 ... (remaining 8193 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.89: 3012 14.89 - 29.77: 198 29.77 - 44.65: 36 44.65 - 59.54: 2 59.54 - 74.42: 2 Dihedral angle restraints: 3250 sinusoidal: 1270 harmonic: 1980 Sorted by residual: dihedral pdb=" CA ASN A 168 " pdb=" C ASN A 168 " pdb=" N TYR A 169 " pdb=" CA TYR A 169 " ideal model delta harmonic sigma weight residual -180.00 -158.44 -21.56 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ASN B 168 " pdb=" C ASN B 168 " pdb=" N TYR B 169 " pdb=" CA TYR B 169 " ideal model delta harmonic sigma weight residual -180.00 -158.47 -21.53 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA SER A 147 " pdb=" C SER A 147 " pdb=" N LEU A 148 " pdb=" CA LEU A 148 " ideal model delta harmonic sigma weight residual 180.00 159.45 20.55 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 3247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 780 0.076 - 0.152: 155 0.152 - 0.228: 17 0.228 - 0.305: 8 0.305 - 0.381: 4 Chirality restraints: 964 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 328 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 328 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" C1 NAG B 406 " pdb=" ND2 ASN B 145 " pdb=" C2 NAG B 406 " pdb=" O5 NAG B 406 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 961 not shown) Planarity restraints: 1006 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 107 " 0.017 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C CYS A 107 " -0.057 2.00e-02 2.50e+03 pdb=" O CYS A 107 " 0.020 2.00e-02 2.50e+03 pdb=" N PHE A 108 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 107 " -0.017 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C CYS B 107 " 0.057 2.00e-02 2.50e+03 pdb=" O CYS B 107 " -0.020 2.00e-02 2.50e+03 pdb=" N PHE B 108 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 100 " 0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO A 101 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 101 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 101 " 0.032 5.00e-02 4.00e+02 ... (remaining 1003 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1822 2.82 - 3.34: 4959 3.34 - 3.86: 10213 3.86 - 4.38: 11600 4.38 - 4.90: 20014 Nonbonded interactions: 48608 Sorted by model distance: nonbonded pdb=" O PHE A 253 " pdb=" OH TYR B 336 " model vdw 2.297 3.040 nonbonded pdb=" OH TYR A 336 " pdb=" O PHE B 253 " model vdw 2.305 3.040 nonbonded pdb=" OH TYR A 283 " pdb=" O TYR A 336 " model vdw 2.305 3.040 nonbonded pdb=" OH TYR B 283 " pdb=" O TYR B 336 " model vdw 2.305 3.040 nonbonded pdb=" OG SER B 319 " pdb=" O GLY B 322 " model vdw 2.344 3.040 ... (remaining 48603 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'J' } 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=0.44 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: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.650 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 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 : 0.008 0.169 6074 Z= 0.344 Angle : 1.078 12.036 8324 Z= 0.518 Chirality : 0.067 0.381 964 Planarity : 0.007 0.058 992 Dihedral : 10.009 74.422 1954 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 0.33 % Allowed : 4.89 % Favored : 94.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.44 (0.27), residues: 660 helix: -2.69 (0.36), residues: 102 sheet: -2.19 (0.39), residues: 172 loop : -3.54 (0.25), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 125 TYR 0.025 0.003 TYR B 128 PHE 0.026 0.003 PHE B 93 TRP 0.013 0.003 TRP B 116 HIS 0.004 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00772 / 0.34 ( 6028) covalent geometry : angle 1.04165 / 0.51 ( 8198) SS BOND : bond 0.00312 / 0.17 ( 12) SS BOND : angle 0.88053 / 0.59 ( 24) hydrogen bonds : bond 0.21892 / 14.48 ( 120) hydrogen bonds : angle 9.02188 / 6.23 ( 312) link_ALPHA1-3 : bond 0.00280 / 0.14 ( 4) link_ALPHA1-3 : angle 1.59151 / 1.10 ( 12) link_ALPHA1-6 : bond 0.00112 / 0.06 ( 2) link_ALPHA1-6 : angle 1.45179 / 1.01 ( 6) link_BETA1-4 : bond 0.01095 / 0.55 ( 14) link_BETA1-4 : angle 2.31312 / 1.29 ( 42) link_NAG-ASN : bond 0.00496 / 0.32 ( 14) link_NAG-ASN : angle 3.40886 / 2.17 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 144 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7764 (pp20) cc_final: 0.7501 (pp20) REVERT: A 155 LYS cc_start: 0.7031 (pmtt) cc_final: 0.5975 (tptt) REVERT: A 316 SER cc_start: 0.8801 (m) cc_final: 0.8557 (p) REVERT: B 95 GLU cc_start: 0.7764 (pp20) cc_final: 0.7478 (pp20) REVERT: B 155 LYS cc_start: 0.7056 (pmtt) cc_final: 0.6018 (tptt) REVERT: B 316 SER cc_start: 0.8775 (m) cc_final: 0.8526 (p) outliers start: 2 outliers final: 2 residues processed: 146 average time/residue: 0.0911 time to fit residues: 16.9914 Evaluate side-chains 83 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain B residue 108 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 HIS B 55 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.126290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.098025 restraints weight = 9207.928| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 3.10 r_work: 0.3178 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6074 Z= 0.171 Angle : 0.752 10.523 8324 Z= 0.357 Chirality : 0.050 0.383 964 Planarity : 0.005 0.040 992 Dihedral : 6.294 45.032 744 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.61 % Allowed : 8.31 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.44 (0.30), residues: 660 helix: -1.17 (0.50), residues: 102 sheet: -1.83 (0.39), residues: 172 loop : -2.94 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 125 TYR 0.017 0.002 TYR A 102 PHE 0.015 0.002 PHE A 78 TRP 0.009 0.001 TRP A 116 HIS 0.003 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 6028) covalent geometry : angle 0.69100 / 0.34 ( 8198) SS BOND : bond 0.00265 / 0.17 ( 12) SS BOND : angle 0.51781 / 0.36 ( 24) hydrogen bonds : bond 0.03892 / 2.78 ( 120) hydrogen bonds : angle 6.43720 / 4.41 ( 312) link_ALPHA1-3 : bond 0.00481 / 0.24 ( 4) link_ALPHA1-3 : angle 1.54131 / 0.93 ( 12) link_ALPHA1-6 : bond 0.00612 / 0.31 ( 2) link_ALPHA1-6 : angle 1.60218 / 1.08 ( 6) link_BETA1-4 : bond 0.00386 / 0.21 ( 14) link_BETA1-4 : angle 1.80156 / 1.13 ( 42) link_NAG-ASN : bond 0.01245 / 0.93 ( 14) link_NAG-ASN : angle 3.78118 / 2.30 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.260 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: symmetry clash REVERT: A 95 GLU cc_start: 0.8120 (pp20) cc_final: 0.7874 (pp20) REVERT: A 197 TYR cc_start: 0.8779 (m-80) cc_final: 0.8354 (m-80) REVERT: A 316 SER cc_start: 0.8924 (m) cc_final: 0.8634 (p) REVERT: B 95 GLU cc_start: 0.8075 (pp20) cc_final: 0.7743 (pp20) REVERT: B 316 SER cc_start: 0.8930 (m) cc_final: 0.8636 (p) outliers start: 16 outliers final: 10 residues processed: 104 average time/residue: 0.0763 time to fit residues: 10.7092 Evaluate side-chains 91 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 233 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 43 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 ASN B 290 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.123975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.097019 restraints weight = 9120.163| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.97 r_work: 0.3179 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6074 Z= 0.182 Angle : 0.707 10.753 8324 Z= 0.332 Chirality : 0.050 0.377 964 Planarity : 0.005 0.038 992 Dihedral : 6.093 51.162 744 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 2.28 % Allowed : 9.93 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -2.99 (0.32), residues: 660 helix: -0.43 (0.57), residues: 102 sheet: -1.65 (0.39), residues: 180 loop : -2.70 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 340 TYR 0.018 0.002 TYR B 197 PHE 0.017 0.002 PHE B 139 TRP 0.010 0.001 TRP A 116 HIS 0.004 0.001 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 ( 6028) covalent geometry : angle 0.65341 / 0.32 ( 8198) SS BOND : bond 0.00326 / 0.21 ( 12) SS BOND : angle 0.49874 / 0.31 ( 24) hydrogen bonds : bond 0.03676 / 2.64 ( 120) hydrogen bonds : angle 5.88091 / 4.08 ( 312) link_ALPHA1-3 : bond 0.00483 / 0.24 ( 4) link_ALPHA1-3 : angle 1.43009 / 0.93 ( 12) link_ALPHA1-6 : bond 0.00490 / 0.25 ( 2) link_ALPHA1-6 : angle 1.58856 / 1.07 ( 6) link_BETA1-4 : bond 0.00427 / 0.24 ( 14) link_BETA1-4 : angle 1.51494 / 0.95 ( 42) link_NAG-ASN : bond 0.00769 / 0.57 ( 14) link_NAG-ASN : angle 3.52231 / 2.15 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.164 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: symmetry clash REVERT: A 95 GLU cc_start: 0.8081 (pp20) cc_final: 0.7839 (pp20) REVERT: A 197 TYR cc_start: 0.8757 (m-80) cc_final: 0.8257 (m-80) REVERT: A 316 SER cc_start: 0.8959 (m) cc_final: 0.8679 (p) REVERT: B 95 GLU cc_start: 0.8081 (pp20) cc_final: 0.7812 (pp20) REVERT: B 316 SER cc_start: 0.8953 (m) cc_final: 0.8651 (p) outliers start: 14 outliers final: 12 residues processed: 97 average time/residue: 0.0708 time to fit residues: 9.2792 Evaluate side-chains 85 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 233 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 13 optimal weight: 0.0060 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 36 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 0.0770 overall best weight: 0.3554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.126415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.099521 restraints weight = 9096.492| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 3.04 r_work: 0.3213 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6074 Z= 0.112 Angle : 0.647 10.524 8324 Z= 0.305 Chirality : 0.047 0.394 964 Planarity : 0.005 0.039 992 Dihedral : 5.830 52.724 744 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 2.12 % Allowed : 11.24 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -2.77 (0.32), residues: 660 helix: -0.20 (0.56), residues: 102 sheet: -1.51 (0.40), residues: 180 loop : -2.58 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 340 TYR 0.014 0.001 TYR B 197 PHE 0.015 0.002 PHE A 151 TRP 0.008 0.001 TRP A 263 HIS 0.002 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 6028) covalent geometry : angle 0.59148 / 0.29 ( 8198) SS BOND : bond 0.00166 / 0.11 ( 12) SS BOND : angle 0.30276 / 0.19 ( 24) hydrogen bonds : bond 0.03184 / 2.27 ( 120) hydrogen bonds : angle 5.52861 / 3.86 ( 312) link_ALPHA1-3 : bond 0.00398 / 0.20 ( 4) link_ALPHA1-3 : angle 1.35976 / 0.89 ( 12) link_ALPHA1-6 : bond 0.00571 / 0.28 ( 2) link_ALPHA1-6 : angle 1.49259 / 1.03 ( 6) link_BETA1-4 : bond 0.00477 / 0.26 ( 14) link_BETA1-4 : angle 1.45572 / 0.88 ( 42) link_NAG-ASN : bond 0.00659 / 0.48 ( 14) link_NAG-ASN : angle 3.41683 / 2.07 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.318 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: symmetry clash REVERT: A 95 GLU cc_start: 0.8153 (pp20) cc_final: 0.7900 (pp20) REVERT: A 197 TYR cc_start: 0.8770 (m-80) cc_final: 0.8304 (m-80) REVERT: A 316 SER cc_start: 0.8991 (m) cc_final: 0.8650 (p) REVERT: B 95 GLU cc_start: 0.8162 (pp20) cc_final: 0.7919 (pp20) REVERT: B 316 SER cc_start: 0.8985 (m) cc_final: 0.8626 (p) outliers start: 13 outliers final: 9 residues processed: 88 average time/residue: 0.0675 time to fit residues: 8.1532 Evaluate side-chains 78 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 217 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 0.0370 chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.124803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.097644 restraints weight = 9269.392| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 3.06 r_work: 0.3195 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6074 Z= 0.139 Angle : 0.647 10.421 8324 Z= 0.304 Chirality : 0.047 0.385 964 Planarity : 0.004 0.037 992 Dihedral : 5.752 53.603 744 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 2.61 % Allowed : 11.40 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -2.64 (0.32), residues: 660 helix: -0.02 (0.57), residues: 102 sheet: -1.39 (0.39), residues: 180 loop : -2.52 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 340 TYR 0.011 0.001 TYR B 169 PHE 0.014 0.002 PHE A 151 TRP 0.008 0.001 TRP A 116 HIS 0.004 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 6028) covalent geometry : angle 0.59546 / 0.29 ( 8198) SS BOND : bond 0.00246 / 0.16 ( 12) SS BOND : angle 0.39986 / 0.27 ( 24) hydrogen bonds : bond 0.03148 / 2.27 ( 120) hydrogen bonds : angle 5.41447 / 3.80 ( 312) link_ALPHA1-3 : bond 0.00447 / 0.22 ( 4) link_ALPHA1-3 : angle 1.42858 / 0.94 ( 12) link_ALPHA1-6 : bond 0.00460 / 0.23 ( 2) link_ALPHA1-6 : angle 1.55080 / 1.05 ( 6) link_BETA1-4 : bond 0.00437 / 0.24 ( 14) link_BETA1-4 : angle 1.38375 / 0.87 ( 42) link_NAG-ASN : bond 0.00656 / 0.49 ( 14) link_NAG-ASN : angle 3.29863 / 1.99 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.182 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 95 GLU cc_start: 0.8154 (pp20) cc_final: 0.7943 (pp20) REVERT: A 197 TYR cc_start: 0.8778 (m-80) cc_final: 0.8288 (m-80) REVERT: A 316 SER cc_start: 0.8982 (m) cc_final: 0.8651 (p) REVERT: B 95 GLU cc_start: 0.8156 (pp20) cc_final: 0.7922 (pp20) REVERT: B 316 SER cc_start: 0.8978 (m) cc_final: 0.8637 (p) outliers start: 16 outliers final: 14 residues processed: 88 average time/residue: 0.0617 time to fit residues: 7.5223 Evaluate side-chains 85 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 341 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 4 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.123950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.096704 restraints weight = 9219.409| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 3.06 r_work: 0.3177 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6074 Z= 0.141 Angle : 0.634 10.188 8324 Z= 0.299 Chirality : 0.047 0.376 964 Planarity : 0.004 0.038 992 Dihedral : 5.702 54.674 744 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 2.44 % Allowed : 12.38 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -2.46 (0.33), residues: 660 helix: 0.13 (0.58), residues: 102 sheet: -1.23 (0.40), residues: 180 loop : -2.43 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 340 TYR 0.012 0.001 TYR A 169 PHE 0.013 0.002 PHE B 139 TRP 0.008 0.001 TRP A 116 HIS 0.003 0.001 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 6028) covalent geometry : angle 0.58475 / 0.29 ( 8198) SS BOND : bond 0.00245 / 0.15 ( 12) SS BOND : angle 0.41395 / 0.29 ( 24) hydrogen bonds : bond 0.03056 / 2.20 ( 120) hydrogen bonds : angle 5.32956 / 3.74 ( 312) link_ALPHA1-3 : bond 0.00437 / 0.22 ( 4) link_ALPHA1-3 : angle 1.43707 / 0.95 ( 12) link_ALPHA1-6 : bond 0.00432 / 0.22 ( 2) link_ALPHA1-6 : angle 1.56310 / 1.06 ( 6) link_BETA1-4 : bond 0.00452 / 0.25 ( 14) link_BETA1-4 : angle 1.31772 / 0.81 ( 42) link_NAG-ASN : bond 0.00648 / 0.48 ( 14) link_NAG-ASN : angle 3.17757 / 1.90 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.201 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 95 GLU cc_start: 0.8180 (pp20) cc_final: 0.7935 (pp20) REVERT: A 197 TYR cc_start: 0.8765 (m-80) cc_final: 0.8303 (m-80) REVERT: A 316 SER cc_start: 0.8975 (m) cc_final: 0.8623 (p) REVERT: B 95 GLU cc_start: 0.8183 (pp20) cc_final: 0.7949 (pp20) REVERT: B 224 LEU cc_start: 0.9314 (mp) cc_final: 0.9106 (mt) REVERT: B 316 SER cc_start: 0.8977 (m) cc_final: 0.8608 (p) outliers start: 15 outliers final: 13 residues processed: 84 average time/residue: 0.0607 time to fit residues: 7.1425 Evaluate side-chains 84 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 341 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 45 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 13 optimal weight: 0.1980 chunk 52 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.123844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.096621 restraints weight = 9258.306| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.05 r_work: 0.3172 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6074 Z= 0.138 Angle : 0.623 10.118 8324 Z= 0.295 Chirality : 0.047 0.374 964 Planarity : 0.004 0.037 992 Dihedral : 5.681 54.995 744 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 2.61 % Allowed : 12.70 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -2.38 (0.33), residues: 660 helix: 0.18 (0.58), residues: 102 sheet: -1.15 (0.40), residues: 180 loop : -2.39 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 340 TYR 0.013 0.001 TYR B 169 PHE 0.016 0.002 PHE A 151 TRP 0.008 0.001 TRP A 116 HIS 0.002 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 6028) covalent geometry : angle 0.57466 / 0.28 ( 8198) SS BOND : bond 0.00245 / 0.15 ( 12) SS BOND : angle 0.39875 / 0.27 ( 24) hydrogen bonds : bond 0.03054 / 2.22 ( 120) hydrogen bonds : angle 5.26437 / 3.69 ( 312) link_ALPHA1-3 : bond 0.00408 / 0.20 ( 4) link_ALPHA1-3 : angle 1.43013 / 0.94 ( 12) link_ALPHA1-6 : bond 0.00467 / 0.23 ( 2) link_ALPHA1-6 : angle 1.57807 / 1.08 ( 6) link_BETA1-4 : bond 0.00448 / 0.25 ( 14) link_BETA1-4 : angle 1.31647 / 0.83 ( 42) link_NAG-ASN : bond 0.00637 / 0.47 ( 14) link_NAG-ASN : angle 3.11602 / 1.86 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.206 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 95 GLU cc_start: 0.8144 (pp20) cc_final: 0.7939 (pp20) REVERT: A 197 TYR cc_start: 0.8753 (m-80) cc_final: 0.8310 (m-80) REVERT: A 316 SER cc_start: 0.8936 (m) cc_final: 0.8595 (p) REVERT: B 95 GLU cc_start: 0.8165 (pp20) cc_final: 0.7945 (pp20) REVERT: B 316 SER cc_start: 0.8962 (m) cc_final: 0.8590 (p) outliers start: 16 outliers final: 14 residues processed: 86 average time/residue: 0.0656 time to fit residues: 7.7784 Evaluate side-chains 83 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 341 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 34 optimal weight: 0.0010 chunk 48 optimal weight: 0.8980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.124437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.097495 restraints weight = 9175.868| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 3.02 r_work: 0.3203 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6074 Z= 0.126 Angle : 0.622 9.985 8324 Z= 0.293 Chirality : 0.047 0.371 964 Planarity : 0.004 0.040 992 Dihedral : 5.621 55.229 744 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 2.77 % Allowed : 13.03 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -2.32 (0.32), residues: 660 helix: 0.20 (0.57), residues: 102 sheet: -1.10 (0.40), residues: 180 loop : -2.35 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 340 TYR 0.012 0.001 TYR A 169 PHE 0.015 0.002 PHE A 151 TRP 0.008 0.001 TRP A 116 HIS 0.002 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 ( 6028) covalent geometry : angle 0.57588 / 0.28 ( 8198) SS BOND : bond 0.00222 / 0.13 ( 12) SS BOND : angle 0.40151 / 0.27 ( 24) hydrogen bonds : bond 0.03010 / 2.17 ( 120) hydrogen bonds : angle 5.16763 / 3.61 ( 312) link_ALPHA1-3 : bond 0.00414 / 0.20 ( 4) link_ALPHA1-3 : angle 1.42909 / 0.94 ( 12) link_ALPHA1-6 : bond 0.00460 / 0.23 ( 2) link_ALPHA1-6 : angle 1.53349 / 1.05 ( 6) link_BETA1-4 : bond 0.00451 / 0.25 ( 14) link_BETA1-4 : angle 1.29956 / 0.82 ( 42) link_NAG-ASN : bond 0.00625 / 0.46 ( 14) link_NAG-ASN : angle 3.05571 / 1.82 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.212 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: symmetry clash REVERT: A 95 GLU cc_start: 0.8133 (pp20) cc_final: 0.7912 (pp20) REVERT: A 197 TYR cc_start: 0.8740 (m-80) cc_final: 0.8292 (m-80) REVERT: A 316 SER cc_start: 0.8958 (m) cc_final: 0.8591 (p) REVERT: B 95 GLU cc_start: 0.8162 (pp20) cc_final: 0.7948 (pp20) REVERT: B 316 SER cc_start: 0.8975 (m) cc_final: 0.8588 (p) outliers start: 17 outliers final: 14 residues processed: 85 average time/residue: 0.0678 time to fit residues: 7.9712 Evaluate side-chains 83 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 341 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 62 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.122047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.095271 restraints weight = 9262.056| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.00 r_work: 0.3170 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6074 Z= 0.165 Angle : 0.661 11.757 8324 Z= 0.309 Chirality : 0.047 0.362 964 Planarity : 0.004 0.037 992 Dihedral : 5.695 55.993 744 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 2.61 % Allowed : 13.19 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -2.29 (0.32), residues: 660 helix: 0.27 (0.58), residues: 102 sheet: -1.06 (0.40), residues: 180 loop : -2.36 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 285 TYR 0.011 0.001 TYR A 169 PHE 0.015 0.002 PHE A 151 TRP 0.008 0.001 TRP A 116 HIS 0.004 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 ( 6028) covalent geometry : angle 0.61909 / 0.30 ( 8198) SS BOND : bond 0.00288 / 0.17 ( 12) SS BOND : angle 0.49615 / 0.34 ( 24) hydrogen bonds : bond 0.03133 / 2.26 ( 120) hydrogen bonds : angle 5.23282 / 3.64 ( 312) link_ALPHA1-3 : bond 0.00392 / 0.19 ( 4) link_ALPHA1-3 : angle 1.46604 / 0.96 ( 12) link_ALPHA1-6 : bond 0.00426 / 0.21 ( 2) link_ALPHA1-6 : angle 1.62740 / 1.11 ( 6) link_BETA1-4 : bond 0.00419 / 0.23 ( 14) link_BETA1-4 : angle 1.28769 / 0.83 ( 42) link_NAG-ASN : bond 0.00620 / 0.46 ( 14) link_NAG-ASN : angle 2.97932 / 1.78 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.203 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 95 GLU cc_start: 0.8121 (pp20) cc_final: 0.7895 (pp20) REVERT: A 197 TYR cc_start: 0.8768 (m-80) cc_final: 0.8323 (m-80) REVERT: A 316 SER cc_start: 0.8948 (m) cc_final: 0.8606 (p) REVERT: B 95 GLU cc_start: 0.8130 (pp20) cc_final: 0.7906 (pp20) REVERT: B 316 SER cc_start: 0.8989 (m) cc_final: 0.8608 (p) outliers start: 16 outliers final: 15 residues processed: 84 average time/residue: 0.0691 time to fit residues: 7.9227 Evaluate side-chains 82 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 341 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.122605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.095910 restraints weight = 9231.068| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.01 r_work: 0.3163 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6074 Z= 0.145 Angle : 0.649 10.843 8324 Z= 0.304 Chirality : 0.047 0.361 964 Planarity : 0.004 0.041 992 Dihedral : 5.692 56.364 744 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.28 % Allowed : 14.17 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -2.27 (0.32), residues: 660 helix: 0.31 (0.58), residues: 102 sheet: -1.06 (0.39), residues: 180 loop : -2.35 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 340 TYR 0.011 0.001 TYR B 169 PHE 0.017 0.002 PHE A 151 TRP 0.007 0.001 TRP A 116 HIS 0.002 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 6028) covalent geometry : angle 0.60722 / 0.30 ( 8198) SS BOND : bond 0.00256 / 0.15 ( 12) SS BOND : angle 0.45305 / 0.31 ( 24) hydrogen bonds : bond 0.03003 / 2.16 ( 120) hydrogen bonds : angle 5.15925 / 3.58 ( 312) link_ALPHA1-3 : bond 0.00396 / 0.20 ( 4) link_ALPHA1-3 : angle 1.44561 / 0.95 ( 12) link_ALPHA1-6 : bond 0.00467 / 0.23 ( 2) link_ALPHA1-6 : angle 1.59925 / 1.10 ( 6) link_BETA1-4 : bond 0.00439 / 0.24 ( 14) link_BETA1-4 : angle 1.27651 / 0.81 ( 42) link_NAG-ASN : bond 0.00608 / 0.45 ( 14) link_NAG-ASN : angle 2.95488 / 1.77 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.243 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 197 TYR cc_start: 0.8751 (m-80) cc_final: 0.8305 (m-80) REVERT: A 316 SER cc_start: 0.8961 (m) cc_final: 0.8620 (p) REVERT: B 95 GLU cc_start: 0.8123 (pp20) cc_final: 0.7920 (pp20) REVERT: B 316 SER cc_start: 0.8966 (m) cc_final: 0.8607 (p) outliers start: 14 outliers final: 14 residues processed: 83 average time/residue: 0.0675 time to fit residues: 7.7613 Evaluate side-chains 80 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 341 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 1 optimal weight: 0.2980 chunk 44 optimal weight: 0.9980 chunk 58 optimal weight: 0.0070 chunk 41 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 34 optimal weight: 0.0040 chunk 13 optimal weight: 0.8980 overall best weight: 0.3610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.124607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.097977 restraints weight = 9084.925| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.03 r_work: 0.3193 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6074 Z= 0.113 Angle : 0.659 10.147 8324 Z= 0.305 Chirality : 0.047 0.360 964 Planarity : 0.004 0.038 992 Dihedral : 5.605 56.392 744 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 2.28 % Allowed : 14.01 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -2.22 (0.32), residues: 660 helix: 0.32 (0.57), residues: 102 sheet: -1.00 (0.39), residues: 180 loop : -2.32 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 340 TYR 0.016 0.001 TYR A 124 PHE 0.017 0.002 PHE A 151 TRP 0.007 0.001 TRP A 263 HIS 0.002 0.001 HIS A 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 6028) covalent geometry : angle 0.61999 / 0.30 ( 8198) SS BOND : bond 0.00200 / 0.12 ( 12) SS BOND : angle 0.36896 / 0.27 ( 24) hydrogen bonds : bond 0.02805 / 1.99 ( 120) hydrogen bonds : angle 5.03391 / 3.48 ( 312) link_ALPHA1-3 : bond 0.00404 / 0.20 ( 4) link_ALPHA1-3 : angle 1.43528 / 0.94 ( 12) link_ALPHA1-6 : bond 0.00496 / 0.25 ( 2) link_ALPHA1-6 : angle 1.49906 / 1.04 ( 6) link_BETA1-4 : bond 0.00470 / 0.26 ( 14) link_BETA1-4 : angle 1.27599 / 0.80 ( 42) link_NAG-ASN : bond 0.00604 / 0.44 ( 14) link_NAG-ASN : angle 2.91623 / 1.74 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1396.05 seconds wall clock time: 24 minutes 53.16 seconds (1493.16 seconds total)