Starting phenix.real_space_refine on Tue Mar 11 14:30:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y3y_10676/03_2025/6y3y_10676.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y3y_10676/03_2025/6y3y_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6y3y_10676/03_2025/6y3y_10676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y3y_10676/03_2025/6y3y_10676.map" model { file = "/net/cci-nas-00/data/ceres_data/6y3y_10676/03_2025/6y3y_10676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y3y_10676/03_2025/6y3y_10676.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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 dihedrals: 12 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 dihedrals: 15 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: G, H, J, B, I 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: 5.17, per 1000 atoms: 0.88 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: 1.74 Conformation dependent library (CDL) restraints added in 750.2 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: 0.64 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: 1.36 Time building geometry restraints manager: 1.96 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 - 21.52: 3720 21.52 - 43.04: 138 43.04 - 64.56: 20 64.56 - 86.07: 38 86.07 - 107.59: 24 Dihedral angle restraints: 3940 sinusoidal: 1960 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 3937 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: 0.03 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'I' } 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: 1.360 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.370 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 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 6028 Z= 0.473 Angle : 1.042 12.036 8198 Z= 0.512 Chirality : 0.067 0.381 964 Planarity : 0.007 0.058 992 Dihedral : 17.088 107.593 2644 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.013 0.003 TRP B 116 HIS 0.004 0.001 HIS B 40 PHE 0.026 0.003 PHE B 93 TYR 0.025 0.003 TYR B 128 ARG 0.004 0.001 ARG B 125 *********************** 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 : 0.642 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: 0.8558 (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: 0.8527 (p) outliers start: 2 outliers final: 2 residues processed: 146 average time/residue: 0.2154 time to fit residues: 39.9256 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 : 0.615 ------------------------------------------------------------------------------- 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 55 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 0.0970 chunk 38 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 98 ASN B 55 HIS B 98 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.127236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.099172 restraints weight = 8981.695| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.06 r_work: 0.3199 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6028 Z= 0.221 Angle : 0.713 8.927 8198 Z= 0.347 Chirality : 0.053 0.425 964 Planarity : 0.005 0.040 992 Dihedral : 15.308 75.299 1434 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 2.61 % Allowed : 7.82 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.30), residues: 660 helix: -1.19 (0.49), residues: 102 sheet: -1.90 (0.39), residues: 176 loop : -2.91 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 116 HIS 0.003 0.001 HIS A 40 PHE 0.015 0.002 PHE A 78 TYR 0.016 0.002 TYR A 102 ARG 0.002 0.000 ARG A 125 *********************** 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 105 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.583 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: 0.8082 (pp20) cc_final: 0.7834 (pp20) REVERT: A 197 TYR cc_start: 0.8772 (m-80) cc_final: 0.8357 (m-80) REVERT: A 316 SER cc_start: 0.8917 (m) cc_final: 0.8624 (p) REVERT: B 95 GLU cc_start: 0.8050 (pp20) cc_final: 0.7742 (pp20) REVERT: B 316 SER cc_start: 0.8937 (m) cc_final: 0.8644 (p) outliers start: 16 outliers final: 10 residues processed: 103 average time/residue: 0.1624 time to fit residues: 22.4161 Evaluate side-chains 90 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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 28 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 32 optimal weight: 0.0570 chunk 57 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3712 r_free = 0.3712 target = 0.123549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.096257 restraints weight = 9164.379| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.06 r_work: 0.3169 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6028 Z= 0.286 Angle : 0.677 8.993 8198 Z= 0.329 Chirality : 0.052 0.428 964 Planarity : 0.005 0.039 992 Dihedral : 11.336 57.852 1434 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 2.77 % Allowed : 9.12 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.32), residues: 660 helix: -0.40 (0.56), residues: 102 sheet: -1.57 (0.39), residues: 180 loop : -2.68 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 116 HIS 0.004 0.001 HIS A 103 PHE 0.020 0.003 PHE B 139 TYR 0.018 0.002 TYR B 197 ARG 0.002 0.001 ARG A 285 *********************** 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 102 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.576 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: 0.8104 (pp20) cc_final: 0.7783 (pp20) REVERT: A 316 SER cc_start: 0.8991 (m) cc_final: 0.8681 (p) REVERT: B 95 GLU cc_start: 0.8132 (pp20) cc_final: 0.7850 (pp20) REVERT: B 316 SER cc_start: 0.8983 (m) cc_final: 0.8660 (p) outliers start: 17 outliers final: 13 residues processed: 100 average time/residue: 0.1703 time to fit residues: 22.7569 Evaluate side-chains 86 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 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 31 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.122755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.095849 restraints weight = 9325.350| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 3.06 r_work: 0.3161 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 6028 Z= 0.253 Angle : 0.638 9.801 8198 Z= 0.312 Chirality : 0.050 0.404 964 Planarity : 0.005 0.040 992 Dihedral : 9.416 55.688 1434 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 1.95 % Allowed : 11.56 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.32), residues: 660 helix: -0.17 (0.56), residues: 102 sheet: -1.51 (0.40), residues: 180 loop : -2.60 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 116 HIS 0.003 0.001 HIS A 103 PHE 0.014 0.002 PHE A 139 TYR 0.014 0.002 TYR B 197 ARG 0.002 0.000 ARG A 262 *********************** 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 88 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.654 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: 0.7883 (pp20) REVERT: A 316 SER cc_start: 0.8987 (m) cc_final: 0.8657 (p) REVERT: B 95 GLU cc_start: 0.8199 (pp20) cc_final: 0.7902 (pp20) REVERT: B 316 SER cc_start: 0.8989 (m) cc_final: 0.8638 (p) REVERT: B 332 ILE cc_start: 0.8903 (mm) cc_final: 0.8664 (tt) outliers start: 12 outliers final: 9 residues processed: 88 average time/residue: 0.1714 time to fit residues: 20.3521 Evaluate side-chains 82 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 224 LEU 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 341 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 2 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 46 optimal weight: 0.0570 chunk 39 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.123436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.096855 restraints weight = 9129.984| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.01 r_work: 0.3172 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 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 = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6028 Z= 0.207 Angle : 0.607 9.634 8198 Z= 0.296 Chirality : 0.049 0.400 964 Planarity : 0.004 0.038 992 Dihedral : 8.425 55.143 1434 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.32), residues: 660 helix: 0.09 (0.57), residues: 102 sheet: -1.35 (0.40), residues: 180 loop : -2.55 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 116 HIS 0.003 0.001 HIS A 299 PHE 0.012 0.002 PHE A 139 TYR 0.014 0.001 TYR A 197 ARG 0.002 0.000 ARG A 340 *********************** 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 91 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.603 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: 0.8177 (pp20) cc_final: 0.7916 (pp20) REVERT: A 316 SER cc_start: 0.8958 (m) cc_final: 0.8632 (p) REVERT: B 95 GLU cc_start: 0.8176 (pp20) cc_final: 0.7925 (pp20) REVERT: B 197 TYR cc_start: 0.8802 (m-80) cc_final: 0.8376 (m-80) REVERT: B 316 SER cc_start: 0.8981 (m) cc_final: 0.8643 (p) outliers start: 16 outliers final: 13 residues processed: 89 average time/residue: 0.1638 time to fit residues: 19.6648 Evaluate side-chains 85 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 185 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 246 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 0.2980 chunk 33 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 65 optimal weight: 0.3980 chunk 64 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.123102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.096711 restraints weight = 9188.962| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.00 r_work: 0.3174 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6028 Z= 0.209 Angle : 0.609 10.911 8198 Z= 0.295 Chirality : 0.049 0.394 964 Planarity : 0.004 0.039 992 Dihedral : 8.017 54.846 1434 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.93 % Allowed : 11.73 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.33), residues: 660 helix: 0.14 (0.57), residues: 102 sheet: -1.18 (0.40), residues: 180 loop : -2.49 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 116 HIS 0.002 0.001 HIS B 103 PHE 0.012 0.002 PHE B 139 TYR 0.013 0.001 TYR B 169 ARG 0.001 0.000 ARG A 285 *********************** 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 91 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.763 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: 0.8147 (pp20) cc_final: 0.7893 (pp20) REVERT: A 316 SER cc_start: 0.8963 (m) cc_final: 0.8630 (p) REVERT: B 95 GLU cc_start: 0.8163 (pp20) cc_final: 0.7959 (pp20) REVERT: B 316 SER cc_start: 0.8995 (m) cc_final: 0.8641 (p) outliers start: 18 outliers final: 15 residues processed: 89 average time/residue: 0.1533 time to fit residues: 18.8019 Evaluate side-chains 83 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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 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 54 optimal weight: 1.9990 chunk 26 optimal weight: 0.0070 chunk 57 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 5 optimal weight: 0.0070 chunk 55 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 0.0980 chunk 40 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.125920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.099255 restraints weight = 9159.904| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.05 r_work: 0.3213 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6028 Z= 0.145 Angle : 0.581 8.520 8198 Z= 0.281 Chirality : 0.048 0.389 964 Planarity : 0.004 0.037 992 Dihedral : 7.609 55.020 1434 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 3.09 % Allowed : 12.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.32), residues: 660 helix: 0.40 (0.58), residues: 100 sheet: -1.13 (0.40), residues: 180 loop : -2.46 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 263 HIS 0.001 0.001 HIS A 40 PHE 0.011 0.001 PHE A 175 TYR 0.018 0.001 TYR A 197 ARG 0.001 0.000 ARG B 340 *********************** 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 97 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.6617 (pmt100) REVERT: A 316 SER cc_start: 0.8964 (m) cc_final: 0.8597 (p) REVERT: B 197 TYR cc_start: 0.8712 (m-80) cc_final: 0.8392 (m-80) REVERT: B 316 SER cc_start: 0.8991 (m) cc_final: 0.8610 (p) outliers start: 19 outliers final: 15 residues processed: 95 average time/residue: 0.1612 time to fit residues: 20.7166 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 : 0.583 ------------------------------------------------------------------------------- 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 262 ARG 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 233 THR 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 45 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 4 optimal weight: 0.0010 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.124042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.097545 restraints weight = 9123.965| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 3.02 r_work: 0.3191 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- 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 = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6028 Z= 0.219 Angle : 0.631 9.390 8198 Z= 0.305 Chirality : 0.049 0.383 964 Planarity : 0.004 0.037 992 Dihedral : 7.572 55.512 1434 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 3.58 % Allowed : 13.52 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.32), residues: 660 helix: 0.49 (0.58), residues: 100 sheet: -1.02 (0.40), residues: 180 loop : -2.46 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 116 HIS 0.003 0.001 HIS A 77 PHE 0.018 0.002 PHE A 73 TYR 0.014 0.001 TYR B 169 ARG 0.002 0.000 ARG A 285 *********************** 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 95 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.623 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: 0.8031 (pp20) cc_final: 0.7783 (pp20) REVERT: A 262 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.6686 (pmt100) REVERT: A 316 SER cc_start: 0.8950 (m) cc_final: 0.8599 (p) REVERT: B 95 GLU cc_start: 0.8024 (pp20) cc_final: 0.7783 (pp20) REVERT: B 224 LEU cc_start: 0.9314 (mp) cc_final: 0.9112 (mt) REVERT: B 316 SER cc_start: 0.8976 (m) cc_final: 0.8611 (p) outliers start: 22 outliers final: 17 residues processed: 93 average time/residue: 0.1723 time to fit residues: 21.6743 Evaluate side-chains 90 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 262 ARG Chi-restraints excluded: chain A residue 273 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 165 ILE 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 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 8 optimal weight: 0.2980 chunk 33 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.123681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.097274 restraints weight = 9145.316| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 3.01 r_work: 0.3187 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- 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 = 0.75 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 = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6028 Z= 0.221 Angle : 0.637 8.430 8198 Z= 0.307 Chirality : 0.048 0.376 964 Planarity : 0.004 0.037 992 Dihedral : 7.521 56.193 1434 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 3.09 % Allowed : 13.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.32), residues: 660 helix: 0.50 (0.58), residues: 100 sheet: -1.12 (0.39), residues: 180 loop : -2.45 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 116 HIS 0.002 0.001 HIS B 23 PHE 0.014 0.002 PHE A 73 TYR 0.015 0.001 TYR A 197 ARG 0.002 0.000 ARG B 340 *********************** 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 92 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.694 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: 0.8091 (pp20) cc_final: 0.7789 (pp20) REVERT: A 262 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.6762 (pmt100) REVERT: A 316 SER cc_start: 0.8959 (m) cc_final: 0.8621 (p) REVERT: B 95 GLU cc_start: 0.8077 (pp20) cc_final: 0.7781 (pp20) REVERT: B 197 TYR cc_start: 0.8717 (m-80) cc_final: 0.8392 (m-80) REVERT: B 224 LEU cc_start: 0.9300 (mp) cc_final: 0.9080 (mt) REVERT: B 316 SER cc_start: 0.8967 (m) cc_final: 0.8619 (p) outliers start: 19 outliers final: 16 residues processed: 90 average time/residue: 0.1693 time to fit residues: 20.6558 Evaluate side-chains 90 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 262 ARG Chi-restraints excluded: chain A residue 273 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 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 31 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.123192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.096929 restraints weight = 9245.666| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.99 r_work: 0.3174 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6028 Z= 0.227 Angle : 0.627 7.879 8198 Z= 0.304 Chirality : 0.048 0.372 964 Planarity : 0.004 0.041 992 Dihedral : 7.479 56.741 1434 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.61 % Allowed : 14.50 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.32), residues: 660 helix: 0.54 (0.58), residues: 100 sheet: -1.13 (0.38), residues: 180 loop : -2.49 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 116 HIS 0.003 0.001 HIS B 23 PHE 0.013 0.002 PHE A 73 TYR 0.020 0.001 TYR A 295 ARG 0.002 0.000 ARG B 340 ********************** 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 91 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.660 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 262 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.6552 (pmt100) REVERT: A 316 SER cc_start: 0.8949 (m) cc_final: 0.8617 (p) REVERT: B 197 TYR cc_start: 0.8709 (m-80) cc_final: 0.8419 (m-80) REVERT: B 316 SER cc_start: 0.8955 (m) cc_final: 0.8614 (p) outliers start: 16 outliers final: 14 residues processed: 91 average time/residue: 0.1686 time to fit residues: 20.7069 Evaluate side-chains 87 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 262 ARG Chi-restraints excluded: chain A residue 273 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 27 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 chunk 53 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 37 optimal weight: 0.0970 chunk 55 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 chunk 25 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.125380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.098829 restraints weight = 9230.820| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.07 r_work: 0.3204 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- 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 = 0.75 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 | |-----------------------------------------------------------------------------| r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6028 Z= 0.160 Angle : 0.612 8.035 8198 Z= 0.297 Chirality : 0.048 0.368 964 Planarity : 0.004 0.039 992 Dihedral : 7.334 56.887 1434 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 2.77 % Allowed : 14.01 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.32), residues: 660 helix: 0.52 (0.57), residues: 100 sheet: -1.05 (0.38), residues: 180 loop : -2.43 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 263 HIS 0.002 0.001 HIS A 23 PHE 0.013 0.002 PHE A 73 TYR 0.020 0.001 TYR A 295 ARG 0.001 0.000 ARG B 340 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2858.69 seconds wall clock time: 50 minutes 3.96 seconds (3003.96 seconds total)