Starting phenix.real_space_refine on Tue Feb 13 11:42:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y3y_10676/02_2024/6y3y_10676.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y3y_10676/02_2024/6y3y_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y3y_10676/02_2024/6y3y_10676.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y3y_10676/02_2024/6y3y_10676.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y3y_10676/02_2024/6y3y_10676.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y3y_10676/02_2024/6y3y_10676.pdb" } 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 Residue "A PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 5854 Number of models: 1 Model: "" Number of chains: 12 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: "B" 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: "G" 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: "H" 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: "I" 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: "J" 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 Chain: "B" 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 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: 3.70, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 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: 2.64 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.58 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: 1.40 Time building geometry restraints manager: 2.83 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: 100.62 - 107.29: 244 107.29 - 113.96: 3316 113.96 - 120.63: 2379 120.63 - 127.31: 2201 127.31 - 133.98: 58 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 2.440 nonbonded pdb=" OH TYR A 336 " pdb=" O PHE B 253 " model vdw 2.305 2.440 nonbonded pdb=" OH TYR A 283 " pdb=" O TYR A 336 " model vdw 2.305 2.440 nonbonded pdb=" OH TYR B 283 " pdb=" O TYR B 336 " model vdw 2.305 2.440 nonbonded pdb=" OG SER B 319 " pdb=" O GLY B 322 " model vdw 2.344 2.440 ... (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 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.700 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 19.650 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.870 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 2 poor density : 144 time to evaluate : 0.636 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: 0.2037 time to fit residues: 37.5376 Evaluate side-chains 83 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 81 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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: 0.0980 chunk 50 optimal weight: 0.2980 chunk 27 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 59 optimal weight: 0.0980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS B 55 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6028 Z= 0.172 Angle : 0.675 8.899 8198 Z= 0.330 Chirality : 0.055 0.565 964 Planarity : 0.005 0.041 992 Dihedral : 15.360 76.434 1434 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 2.61 % Allowed : 8.14 % Favored : 89.25 % 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: -3.46 (0.30), residues: 660 helix: -1.13 (0.49), residues: 102 sheet: -1.87 (0.38), residues: 176 loop : -2.97 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 116 HIS 0.003 0.001 HIS A 40 PHE 0.015 0.002 PHE A 78 TYR 0.016 0.001 TYR A 102 ARG 0.001 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 104 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 0.811 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: 0.7806 (pp20) cc_final: 0.7449 (pp20) REVERT: A 155 LYS cc_start: 0.6879 (pmtt) cc_final: 0.5955 (tptt) REVERT: A 197 TYR cc_start: 0.8505 (m-80) cc_final: 0.8099 (m-80) REVERT: A 316 SER cc_start: 0.8699 (m) cc_final: 0.8431 (p) REVERT: B 95 GLU cc_start: 0.7787 (pp20) cc_final: 0.7390 (pp20) REVERT: B 155 LYS cc_start: 0.6901 (pmtt) cc_final: 0.5996 (tptt) REVERT: B 316 SER cc_start: 0.8715 (m) cc_final: 0.8469 (p) outliers start: 16 outliers final: 10 residues processed: 102 average time/residue: 0.1824 time to fit residues: 24.6683 Evaluate side-chains 86 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 33 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6028 Z= 0.256 Angle : 0.660 10.786 8198 Z= 0.315 Chirality : 0.051 0.430 964 Planarity : 0.005 0.035 992 Dihedral : 11.719 60.036 1434 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 2.61 % Allowed : 10.10 % Favored : 87.30 % 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: -2.94 (0.31), residues: 660 helix: -0.42 (0.55), residues: 102 sheet: -1.54 (0.38), residues: 180 loop : -2.71 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 116 HIS 0.003 0.001 HIS A 299 PHE 0.017 0.002 PHE A 329 TYR 0.014 0.002 TYR B 102 ARG 0.005 0.001 ARG A 340 *********************** 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 101 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 0.664 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: 0.7781 (pp20) cc_final: 0.7353 (pp20) REVERT: A 316 SER cc_start: 0.8703 (m) cc_final: 0.8450 (p) REVERT: B 95 GLU cc_start: 0.7784 (pp20) cc_final: 0.7375 (pp20) REVERT: B 316 SER cc_start: 0.8695 (m) cc_final: 0.8418 (p) outliers start: 16 outliers final: 13 residues processed: 99 average time/residue: 0.1722 time to fit residues: 22.7785 Evaluate side-chains 86 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 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 59 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 chunk 53 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6028 Z= 0.234 Angle : 0.622 8.561 8198 Z= 0.301 Chirality : 0.050 0.411 964 Planarity : 0.004 0.038 992 Dihedral : 9.258 54.752 1434 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 2.77 % Allowed : 10.91 % Favored : 86.32 % 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: -2.69 (0.32), residues: 660 helix: -0.02 (0.57), residues: 102 sheet: -1.41 (0.39), residues: 180 loop : -2.58 (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 40 PHE 0.015 0.002 PHE A 139 TYR 0.018 0.002 TYR B 295 ARG 0.005 0.000 ARG A 340 *********************** 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 92 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 75 time to evaluate : 0.613 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: 0.7759 (pp20) cc_final: 0.7340 (pp20) REVERT: A 197 TYR cc_start: 0.8525 (m-80) cc_final: 0.8050 (m-80) REVERT: A 316 SER cc_start: 0.8710 (m) cc_final: 0.8451 (p) REVERT: B 95 GLU cc_start: 0.7757 (pp20) cc_final: 0.7347 (pp20) REVERT: B 316 SER cc_start: 0.8709 (m) cc_final: 0.8421 (p) outliers start: 17 outliers final: 13 residues processed: 89 average time/residue: 0.1686 time to fit residues: 20.1660 Evaluate side-chains 84 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 224 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 242 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 114 ASP 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 36 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 0.2980 chunk 26 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2933 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= 0.190 Angle : 0.595 9.766 8198 Z= 0.288 Chirality : 0.049 0.401 964 Planarity : 0.004 0.038 992 Dihedral : 8.369 54.509 1434 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 2.44 % Allowed : 11.24 % Favored : 86.32 % 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: -2.51 (0.32), residues: 660 helix: 0.08 (0.57), residues: 102 sheet: -1.25 (0.39), residues: 180 loop : -2.48 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 116 HIS 0.002 0.001 HIS A 299 PHE 0.015 0.002 PHE B 151 TYR 0.014 0.001 TYR B 295 ARG 0.004 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 87 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.687 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: 0.7697 (pp20) cc_final: 0.7301 (pp20) REVERT: A 197 TYR cc_start: 0.8518 (m-80) cc_final: 0.8021 (m-80) REVERT: A 316 SER cc_start: 0.8708 (m) cc_final: 0.8431 (p) REVERT: B 95 GLU cc_start: 0.7689 (pp20) cc_final: 0.7299 (pp20) REVERT: B 316 SER cc_start: 0.8720 (m) cc_final: 0.8442 (p) outliers start: 15 outliers final: 12 residues processed: 85 average time/residue: 0.1592 time to fit residues: 18.5394 Evaluate side-chains 82 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 114 ASP 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 341 CYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 217 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 0.0770 chunk 15 optimal weight: 0.0170 chunk 63 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 0.0020 chunk 21 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6028 Z= 0.151 Angle : 0.574 8.503 8198 Z= 0.276 Chirality : 0.048 0.394 964 Planarity : 0.004 0.038 992 Dihedral : 7.642 53.891 1434 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 3.09 % Allowed : 11.89 % Favored : 85.02 % 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: -2.32 (0.32), residues: 660 helix: 0.35 (0.58), residues: 100 sheet: -1.05 (0.39), residues: 180 loop : -2.42 (0.30), 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 40 PHE 0.011 0.001 PHE A 151 TYR 0.020 0.001 TYR B 295 ARG 0.002 0.000 ARG B 340 *********************** 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 93 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 74 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7655 (pp20) cc_final: 0.7273 (pp20) REVERT: A 197 TYR cc_start: 0.8526 (m-80) cc_final: 0.8066 (m-80) REVERT: A 316 SER cc_start: 0.8702 (m) cc_final: 0.8427 (p) REVERT: A 332 ILE cc_start: 0.8794 (mm) cc_final: 0.8581 (tt) REVERT: B 95 GLU cc_start: 0.7682 (pp20) cc_final: 0.7308 (pp20) outliers start: 19 outliers final: 14 residues processed: 89 average time/residue: 0.1527 time to fit residues: 18.7795 Evaluate side-chains 82 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 68 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 114 ASP 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 114 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 273 LEU 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 46 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 0.0770 chunk 37 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3250 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= 0.207 Angle : 0.577 9.893 8198 Z= 0.279 Chirality : 0.048 0.387 964 Planarity : 0.004 0.038 992 Dihedral : 7.537 54.252 1434 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % 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: -2.27 (0.32), residues: 660 helix: 0.24 (0.57), residues: 102 sheet: -0.97 (0.39), residues: 180 loop : -2.38 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 116 HIS 0.002 0.001 HIS B 299 PHE 0.017 0.002 PHE A 329 TYR 0.014 0.001 TYR B 295 ARG 0.004 0.000 ARG A 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 86 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 67 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: A 95 GLU cc_start: 0.7708 (pp20) cc_final: 0.7313 (pp20) REVERT: A 197 TYR cc_start: 0.8560 (m-80) cc_final: 0.8105 (m-80) REVERT: A 332 ILE cc_start: 0.8808 (mm) cc_final: 0.8582 (tt) REVERT: B 95 GLU cc_start: 0.7694 (pp20) cc_final: 0.7311 (pp20) outliers start: 19 outliers final: 17 residues processed: 82 average time/residue: 0.1502 time to fit residues: 17.1971 Evaluate side-chains 83 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 66 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 114 ASP 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 114 ASP 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 273 LEU 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 12 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 5 optimal weight: 0.0050 chunk 50 optimal weight: 0.5980 chunk 57 optimal weight: 0.3980 chunk 60 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 59 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3371 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= 0.166 Angle : 0.560 9.410 8198 Z= 0.270 Chirality : 0.047 0.379 964 Planarity : 0.004 0.038 992 Dihedral : 7.274 54.420 1434 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 3.42 % Allowed : 11.89 % 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: -2.15 (0.33), residues: 660 helix: 0.43 (0.58), residues: 100 sheet: -0.85 (0.40), residues: 180 loop : -2.34 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 116 HIS 0.002 0.001 HIS A 299 PHE 0.015 0.002 PHE A 329 TYR 0.016 0.001 TYR B 295 ARG 0.001 0.000 ARG A 340 *********************** 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 88 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 67 time to evaluate : 0.643 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: 0.7623 (pp20) cc_final: 0.7248 (pp20) REVERT: A 197 TYR cc_start: 0.8529 (m-80) cc_final: 0.8083 (m-80) REVERT: A 332 ILE cc_start: 0.8779 (mm) cc_final: 0.8568 (tt) REVERT: B 95 GLU cc_start: 0.7604 (pp20) cc_final: 0.7246 (pp20) outliers start: 21 outliers final: 17 residues processed: 85 average time/residue: 0.1460 time to fit residues: 17.3544 Evaluate side-chains 78 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 61 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 114 ASP 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 233 THR 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 114 ASP 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 273 LEU 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 25 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 38 optimal weight: 0.0970 chunk 62 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3448 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= 0.184 Angle : 0.571 9.642 8198 Z= 0.275 Chirality : 0.048 0.374 964 Planarity : 0.004 0.038 992 Dihedral : 7.226 54.555 1434 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 3.26 % Allowed : 13.84 % 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: -2.13 (0.33), residues: 660 helix: 0.48 (0.57), residues: 100 sheet: -0.82 (0.39), residues: 180 loop : -2.35 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 116 HIS 0.001 0.000 HIS A 299 PHE 0.018 0.002 PHE B 151 TYR 0.011 0.001 TYR B 295 ARG 0.004 0.000 ARG A 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 86 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 66 time to evaluate : 0.659 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: 0.7632 (pp20) cc_final: 0.7250 (pp20) REVERT: A 197 TYR cc_start: 0.8542 (m-80) cc_final: 0.8103 (m-80) REVERT: A 332 ILE cc_start: 0.8779 (mm) cc_final: 0.8571 (tt) REVERT: B 95 GLU cc_start: 0.7619 (pp20) cc_final: 0.7248 (pp20) REVERT: B 131 MET cc_start: 0.9065 (tpp) cc_final: 0.8837 (mmp) outliers start: 20 outliers final: 17 residues processed: 83 average time/residue: 0.1503 time to fit residues: 17.3314 Evaluate side-chains 80 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 63 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 114 ASP 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 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 273 LEU 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 60 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 5 optimal weight: 0.0000 chunk 40 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6028 Z= 0.186 Angle : 0.574 9.427 8198 Z= 0.277 Chirality : 0.047 0.369 964 Planarity : 0.004 0.038 992 Dihedral : 7.171 54.894 1434 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 3.09 % Allowed : 14.17 % Favored : 82.74 % 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: -2.11 (0.33), residues: 660 helix: 0.40 (0.57), residues: 102 sheet: -0.84 (0.39), residues: 180 loop : -2.30 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 116 HIS 0.001 0.001 HIS B 299 PHE 0.018 0.002 PHE B 151 TYR 0.013 0.001 TYR B 221 ARG 0.001 0.000 ARG A 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 83 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 64 time to evaluate : 0.645 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: 0.7625 (pp20) cc_final: 0.7246 (pp20) REVERT: A 197 TYR cc_start: 0.8538 (m-80) cc_final: 0.8101 (m-80) REVERT: A 224 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9099 (mt) REVERT: A 332 ILE cc_start: 0.8784 (mm) cc_final: 0.8572 (tt) REVERT: B 95 GLU cc_start: 0.7609 (pp20) cc_final: 0.7242 (pp20) REVERT: B 131 MET cc_start: 0.9084 (tpp) cc_final: 0.8839 (mmp) outliers start: 19 outliers final: 17 residues processed: 80 average time/residue: 0.1520 time to fit residues: 16.9493 Evaluate side-chains 79 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 61 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 114 ASP 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 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 273 LEU 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 52 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.122078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.095545 restraints weight = 9103.340| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.95 r_work: 0.3154 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- 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 = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6028 Z= 0.266 Angle : 0.609 11.075 8198 Z= 0.295 Chirality : 0.047 0.360 964 Planarity : 0.004 0.038 992 Dihedral : 7.245 55.421 1434 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 2.77 % Allowed : 14.33 % 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: -2.16 (0.33), residues: 660 helix: 0.43 (0.57), residues: 102 sheet: -0.86 (0.38), residues: 180 loop : -2.36 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 116 HIS 0.002 0.001 HIS A 299 PHE 0.020 0.002 PHE B 151 TYR 0.020 0.002 TYR B 295 ARG 0.004 0.000 ARG A 340 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1649.09 seconds wall clock time: 30 minutes 32.74 seconds (1832.74 seconds total)