Starting phenix.real_space_refine on Sat Jul 4 09:33:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pr5_71798/07_2026/9pr5_71798_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pr5_71798/07_2026/9pr5_71798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pr5_71798/07_2026/9pr5_71798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pr5_71798/07_2026/9pr5_71798.map" model { file = "/net/cci-nas-00/data/ceres_data/9pr5_71798/07_2026/9pr5_71798_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pr5_71798/07_2026/9pr5_71798_trim.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 72 5.16 5 C 6256 2.51 5 N 1548 2.21 5 O 1780 1.98 5 H 9248 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18916 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 4661 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 15, 'TRANS': 279} Chain breaks: 2 Chain: "B" Number of atoms: 4661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 4661 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 15, 'TRANS': 279} Chain breaks: 2 Chain: "C" Number of atoms: 4661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 4661 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 15, 'TRANS': 279} Chain breaks: 2 Chain: "D" Number of atoms: 4661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 4661 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 15, 'TRANS': 279} Chain breaks: 2 Chain: "A" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 96 Unusual residues: {'CLR': 2, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "B" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 68 Unusual residues: {'CLR': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "C" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 68 Unusual residues: {'CLR': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 2.96, per 1000 atoms: 0.16 Number of scatterers: 18916 At special positions: 0 Unit cell: (95.25, 96.2025, 123.825, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 72 16.00 P 12 15.00 O 1780 8.00 N 1548 7.00 C 6256 6.00 H 9248 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 131 " distance=2.03 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 131 " distance=2.03 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 131 " distance=2.03 Simple disulfide: pdb=" SG CYS D 99 " - pdb=" SG CYS D 131 " 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 Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 580.4 milliseconds 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2240 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 24 sheets defined 38.6% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 40 through 43 Processing helix chain 'A' and resid 44 through 51 removed outlier: 3.885A pdb=" N LEU A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 83 removed outlier: 4.216A pdb=" N PHE A 64 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 87 Processing helix chain 'A' and resid 105 through 118 Processing helix chain 'A' and resid 131 through 159 removed outlier: 3.717A pdb=" N ILE A 135 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 161 No H-bonds generated for 'chain 'A' and resid 160 through 161' Processing helix chain 'A' and resid 162 through 166 removed outlier: 4.163A pdb=" N ASN A 165 " --> pdb=" O ARG A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 259 removed outlier: 4.037A pdb=" N THR A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU A 256 " --> pdb=" O PRO A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 291 No H-bonds generated for 'chain 'A' and resid 289 through 291' Processing helix chain 'A' and resid 315 through 318 Processing helix chain 'B' and resid 40 through 43 Processing helix chain 'B' and resid 44 through 51 removed outlier: 3.885A pdb=" N LEU B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 83 removed outlier: 4.215A pdb=" N PHE B 64 " --> pdb=" O PHE B 60 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL B 65 " --> pdb=" O SER B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 87 Processing helix chain 'B' and resid 105 through 118 Processing helix chain 'B' and resid 131 through 159 removed outlier: 3.716A pdb=" N ILE B 135 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 161 No H-bonds generated for 'chain 'B' and resid 160 through 161' Processing helix chain 'B' and resid 162 through 166 removed outlier: 4.163A pdb=" N ASN B 165 " --> pdb=" O ARG B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 259 removed outlier: 4.037A pdb=" N THR B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU B 256 " --> pdb=" O PRO B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 291 No H-bonds generated for 'chain 'B' and resid 289 through 291' Processing helix chain 'B' and resid 315 through 318 Processing helix chain 'C' and resid 40 through 43 Processing helix chain 'C' and resid 44 through 51 removed outlier: 3.886A pdb=" N LEU C 48 " --> pdb=" O ALA C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 83 removed outlier: 4.215A pdb=" N PHE C 64 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL C 65 " --> pdb=" O SER C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 87 Processing helix chain 'C' and resid 105 through 118 Processing helix chain 'C' and resid 131 through 159 removed outlier: 3.717A pdb=" N ILE C 135 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL C 157 " --> pdb=" O THR C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 161 No H-bonds generated for 'chain 'C' and resid 160 through 161' Processing helix chain 'C' and resid 162 through 166 removed outlier: 4.163A pdb=" N ASN C 165 " --> pdb=" O ARG C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 259 removed outlier: 4.037A pdb=" N THR C 255 " --> pdb=" O SER C 251 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU C 256 " --> pdb=" O PRO C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 291 No H-bonds generated for 'chain 'C' and resid 289 through 291' Processing helix chain 'C' and resid 315 through 318 Processing helix chain 'D' and resid 40 through 43 Processing helix chain 'D' and resid 44 through 51 removed outlier: 3.886A pdb=" N LEU D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 83 removed outlier: 4.216A pdb=" N PHE D 64 " --> pdb=" O PHE D 60 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL D 65 " --> pdb=" O SER D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 87 Processing helix chain 'D' and resid 105 through 118 Processing helix chain 'D' and resid 131 through 159 removed outlier: 3.716A pdb=" N ILE D 135 " --> pdb=" O CYS D 131 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL D 157 " --> pdb=" O THR D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 161 No H-bonds generated for 'chain 'D' and resid 160 through 161' Processing helix chain 'D' and resid 162 through 166 removed outlier: 4.163A pdb=" N ASN D 165 " --> pdb=" O ARG D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 259 removed outlier: 4.037A pdb=" N THR D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU D 256 " --> pdb=" O PRO D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 291 No H-bonds generated for 'chain 'D' and resid 289 through 291' Processing helix chain 'D' and resid 315 through 318 Processing sheet with id=AA1, first strand: chain 'A' and resid 170 through 172 Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 172 removed outlier: 6.679A pdb=" N ALA A 176 " --> pdb=" O MET A 294 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 217 through 221 removed outlier: 6.847A pdb=" N THR A 200 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N PHE A 236 " --> pdb=" O THR A 200 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 217 through 221 removed outlier: 5.605A pdb=" N SER A 201 " --> pdb=" O MET A 274 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N MET A 274 " --> pdb=" O SER A 201 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 297 through 299 Processing sheet with id=AA6, first strand: chain 'A' and resid 303 through 305 Processing sheet with id=AA7, first strand: chain 'B' and resid 170 through 172 Processing sheet with id=AA8, first strand: chain 'B' and resid 170 through 172 removed outlier: 6.679A pdb=" N ALA B 176 " --> pdb=" O MET B 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 217 through 221 removed outlier: 6.848A pdb=" N THR B 200 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N PHE B 236 " --> pdb=" O THR B 200 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 217 through 221 removed outlier: 5.606A pdb=" N SER B 201 " --> pdb=" O MET B 274 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N MET B 274 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 297 through 299 Processing sheet with id=AB3, first strand: chain 'B' and resid 303 through 305 Processing sheet with id=AB4, first strand: chain 'C' and resid 170 through 172 Processing sheet with id=AB5, first strand: chain 'C' and resid 170 through 172 removed outlier: 6.680A pdb=" N ALA C 176 " --> pdb=" O MET C 294 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 217 through 222 removed outlier: 4.506A pdb=" N ALA C 206 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR C 200 " --> pdb=" O PHE C 236 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE C 236 " --> pdb=" O THR C 200 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 217 through 222 removed outlier: 4.506A pdb=" N ALA C 206 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N SER C 201 " --> pdb=" O MET C 274 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N MET C 274 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 297 through 299 Processing sheet with id=AB9, first strand: chain 'C' and resid 303 through 305 Processing sheet with id=AC1, first strand: chain 'D' and resid 170 through 172 Processing sheet with id=AC2, first strand: chain 'D' and resid 170 through 172 removed outlier: 6.679A pdb=" N ALA D 176 " --> pdb=" O MET D 294 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 217 through 222 removed outlier: 4.506A pdb=" N ALA D 206 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR D 200 " --> pdb=" O PHE D 236 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE D 236 " --> pdb=" O THR D 200 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 217 through 222 removed outlier: 4.506A pdb=" N ALA D 206 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N SER D 201 " --> pdb=" O MET D 274 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N MET D 274 " --> pdb=" O SER D 201 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 297 through 299 Processing sheet with id=AC6, first strand: chain 'D' and resid 303 through 305 464 hydrogen bonds defined for protein. 1296 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: 3.84 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9236 1.03 - 1.23: 20 1.23 - 1.42: 4180 1.42 - 1.62: 5604 1.62 - 1.81: 140 Bond restraints: 19180 Sorted by residual: bond pdb=" C1A PIO A 401 " pdb=" O2C PIO A 401 " ideal model delta sigma weight residual 1.332 1.407 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C1A PIO C 401 " pdb=" O2C PIO C 401 " ideal model delta sigma weight residual 1.332 1.407 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C1A PIO D 401 " pdb=" O2C PIO D 401 " ideal model delta sigma weight residual 1.332 1.406 -0.074 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C1A PIO B 401 " pdb=" O2C PIO B 401 " ideal model delta sigma weight residual 1.332 1.406 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" O43 PIO A 401 " pdb=" P4 PIO A 401 " ideal model delta sigma weight residual 1.529 1.459 0.070 2.00e-02 2.50e+03 1.21e+01 ... (remaining 19175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.23: 34404 4.23 - 8.45: 44 8.45 - 12.68: 37 12.68 - 16.90: 7 16.90 - 21.13: 4 Bond angle restraints: 34496 Sorted by residual: angle pdb=" O11 PIO D 401 " pdb=" P1 PIO D 401 " pdb=" O12 PIO D 401 " ideal model delta sigma weight residual 121.09 99.96 21.13 3.00e+00 1.11e-01 4.96e+01 angle pdb=" O11 PIO C 401 " pdb=" P1 PIO C 401 " pdb=" O12 PIO C 401 " ideal model delta sigma weight residual 121.09 99.97 21.12 3.00e+00 1.11e-01 4.96e+01 angle pdb=" O11 PIO A 401 " pdb=" P1 PIO A 401 " pdb=" O12 PIO A 401 " ideal model delta sigma weight residual 121.09 99.97 21.12 3.00e+00 1.11e-01 4.96e+01 angle pdb=" O11 PIO B 401 " pdb=" P1 PIO B 401 " pdb=" O12 PIO B 401 " ideal model delta sigma weight residual 121.09 100.03 21.06 3.00e+00 1.11e-01 4.93e+01 angle pdb=" O1 PIO C 401 " pdb=" P1 PIO C 401 " pdb=" O13 PIO C 401 " ideal model delta sigma weight residual 97.64 111.96 -14.32 3.00e+00 1.11e-01 2.28e+01 ... (remaining 34491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.24: 8580 15.24 - 30.49: 480 30.49 - 45.73: 128 45.73 - 60.97: 112 60.97 - 76.22: 12 Dihedral angle restraints: 9312 sinusoidal: 5052 harmonic: 4260 Sorted by residual: dihedral pdb=" CA ARG A 162 " pdb=" C ARG A 162 " pdb=" N PRO A 163 " pdb=" CA PRO A 163 " ideal model delta harmonic sigma weight residual 180.00 160.82 19.18 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ARG B 162 " pdb=" C ARG B 162 " pdb=" N PRO B 163 " pdb=" CA PRO B 163 " ideal model delta harmonic sigma weight residual 180.00 160.85 19.15 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ARG C 162 " pdb=" C ARG C 162 " pdb=" N PRO C 163 " pdb=" CA PRO C 163 " ideal model delta harmonic sigma weight residual 180.00 160.86 19.14 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 9309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 871 0.025 - 0.049: 429 0.049 - 0.074: 100 0.074 - 0.099: 76 0.099 - 0.123: 56 Chirality restraints: 1532 Sorted by residual: chirality pdb=" CA ILE A 170 " pdb=" N ILE A 170 " pdb=" C ILE A 170 " pdb=" CB ILE A 170 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CA ILE C 170 " pdb=" N ILE C 170 " pdb=" C ILE C 170 " pdb=" CB ILE C 170 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CA ILE D 170 " pdb=" N ILE D 170 " pdb=" C ILE D 170 " pdb=" CB ILE D 170 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 ... (remaining 1529 not shown) Planarity restraints: 2764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 162 " -0.040 5.00e-02 4.00e+02 6.11e-02 5.97e+00 pdb=" N PRO C 163 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO C 163 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 163 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 162 " 0.040 5.00e-02 4.00e+02 6.09e-02 5.94e+00 pdb=" N PRO A 163 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 162 " 0.040 5.00e-02 4.00e+02 6.08e-02 5.92e+00 pdb=" N PRO D 163 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO D 163 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 163 " 0.034 5.00e-02 4.00e+02 ... (remaining 2761 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.45: 10357 2.45 - 2.99: 40737 2.99 - 3.53: 45519 3.53 - 4.06: 60954 4.06 - 4.60: 87929 Nonbonded interactions: 245496 Sorted by model distance: nonbonded pdb=" H VAL C 157 " pdb=" H ALA C 158 " model vdw 1.914 2.100 nonbonded pdb=" H VAL D 157 " pdb=" H ALA D 158 " model vdw 1.914 2.100 nonbonded pdb=" H VAL A 157 " pdb=" H ALA A 158 " model vdw 1.914 2.100 nonbonded pdb=" H VAL B 157 " pdb=" H ALA B 158 " model vdw 1.915 2.100 nonbonded pdb=" HD2 ARG C 203 " pdb="HH11 ARG C 203 " model vdw 1.934 2.270 ... (remaining 245491 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 19 through 401) selection = (chain 'B' and resid 19 through 401) selection = (chain 'C' and resid 19 through 401) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 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: 0.110 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.100 Find NCS groups from input model: 0.210 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 9936 Z= 0.255 Angle : 0.985 21.131 13532 Z= 0.404 Chirality : 0.039 0.123 1532 Planarity : 0.004 0.061 1656 Dihedral : 10.526 68.619 3744 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.77 % Allowed : 3.09 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.27), residues: 1156 helix: 1.66 (0.26), residues: 348 sheet: -0.35 (0.32), residues: 304 loop : 0.76 (0.33), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 203 TYR 0.008 0.001 TYR C 288 PHE 0.008 0.001 PHE A 71 TRP 0.003 0.001 TRP C 45 HIS 0.003 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.26 ( 9932) covalent geometry : angle 0.98503 / 0.40 (13524) SS BOND : bond 0.00164 / 0.08 ( 4) SS BOND : angle 0.38730 / 0.22 ( 8) hydrogen bonds : bond 0.13493 / 8.48 ( 438) hydrogen bonds : angle 6.96152 / 4.93 ( 1296) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 315 time to evaluate : 0.475 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASP cc_start: 0.6871 (m-30) cc_final: 0.6567 (m-30) REVERT: A 171 ARG cc_start: 0.7720 (ttt180) cc_final: 0.7353 (ttt180) REVERT: A 184 LYS cc_start: 0.8567 (tptp) cc_final: 0.8103 (tptt) REVERT: A 224 PHE cc_start: 0.8080 (m-80) cc_final: 0.7851 (m-80) REVERT: A 239 PHE cc_start: 0.7780 (p90) cc_final: 0.7541 (p90) REVERT: A 245 HIS cc_start: 0.6916 (t70) cc_final: 0.6699 (t70) REVERT: A 268 VAL cc_start: 0.8669 (p) cc_final: 0.8429 (m) REVERT: A 288 TYR cc_start: 0.7243 (m-80) cc_final: 0.7021 (m-80) REVERT: A 289 LEU cc_start: 0.8777 (mt) cc_final: 0.8538 (mt) REVERT: B 84 ASP cc_start: 0.6864 (m-30) cc_final: 0.6615 (m-30) REVERT: B 171 ARG cc_start: 0.7808 (ttt180) cc_final: 0.7425 (ttt180) REVERT: B 184 LYS cc_start: 0.8558 (tptp) cc_final: 0.8156 (tptt) REVERT: B 239 PHE cc_start: 0.7840 (p90) cc_final: 0.7574 (p90) REVERT: B 245 HIS cc_start: 0.6939 (t70) cc_final: 0.6732 (t70) REVERT: B 268 VAL cc_start: 0.8695 (p) cc_final: 0.8433 (m) REVERT: B 275 GLN cc_start: 0.7670 (mm110) cc_final: 0.7288 (mm110) REVERT: B 284 ARG cc_start: 0.5367 (tpt170) cc_final: 0.4403 (tpp80) REVERT: B 288 TYR cc_start: 0.7202 (m-80) cc_final: 0.6950 (m-80) REVERT: B 289 LEU cc_start: 0.8773 (mt) cc_final: 0.8568 (mm) REVERT: C 81 MET cc_start: 0.7344 (mtp) cc_final: 0.7009 (mtp) REVERT: C 84 ASP cc_start: 0.6891 (m-30) cc_final: 0.6663 (m-30) REVERT: C 171 ARG cc_start: 0.7761 (ttt180) cc_final: 0.7406 (ttt180) REVERT: C 186 ASN cc_start: 0.6772 (m-40) cc_final: 0.6158 (m-40) REVERT: C 224 PHE cc_start: 0.8194 (m-80) cc_final: 0.7982 (m-80) REVERT: C 239 PHE cc_start: 0.7818 (p90) cc_final: 0.7558 (p90) REVERT: C 245 HIS cc_start: 0.6872 (t70) cc_final: 0.6637 (t70) REVERT: C 268 VAL cc_start: 0.8681 (p) cc_final: 0.8404 (m) REVERT: C 275 GLN cc_start: 0.7662 (mm110) cc_final: 0.7283 (mm110) REVERT: C 284 ARG cc_start: 0.5228 (tpt170) cc_final: 0.4318 (tpp80) REVERT: C 289 LEU cc_start: 0.8811 (mt) cc_final: 0.8590 (mm) REVERT: D 81 MET cc_start: 0.7490 (mtp) cc_final: 0.7135 (mtp) REVERT: D 82 ASN cc_start: 0.7927 (t0) cc_final: 0.7551 (t0) REVERT: D 84 ASP cc_start: 0.6948 (m-30) cc_final: 0.6738 (m-30) REVERT: D 171 ARG cc_start: 0.7760 (ttt180) cc_final: 0.7437 (ttt180) REVERT: D 223 ASP cc_start: 0.7665 (t0) cc_final: 0.7454 (t0) REVERT: D 224 PHE cc_start: 0.8083 (m-80) cc_final: 0.7856 (m-80) REVERT: D 268 VAL cc_start: 0.8725 (p) cc_final: 0.8518 (m) REVERT: D 269 VAL cc_start: 0.8386 (t) cc_final: 0.8184 (m) REVERT: D 275 GLN cc_start: 0.7461 (mm110) cc_final: 0.7006 (mm110) REVERT: D 284 ARG cc_start: 0.5288 (tpt170) cc_final: 0.4368 (tpp80) REVERT: D 288 TYR cc_start: 0.7168 (m-80) cc_final: 0.6903 (m-80) outliers start: 8 outliers final: 4 residues processed: 319 average time/residue: 0.1871 time to fit residues: 84.0429 Evaluate side-chains 296 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 292 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain D residue 210 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 275 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.186235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.146377 restraints weight = 43427.304| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.90 r_work: 0.3631 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9936 Z= 0.199 Angle : 0.574 4.916 13532 Z= 0.299 Chirality : 0.042 0.132 1532 Planarity : 0.005 0.055 1656 Dihedral : 7.904 81.776 1572 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.87 % Allowed : 10.71 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.26), residues: 1156 helix: 1.06 (0.26), residues: 380 sheet: -0.14 (0.33), residues: 252 loop : 0.58 (0.32), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 203 TYR 0.012 0.002 TYR D 288 PHE 0.021 0.002 PHE B 270 TRP 0.006 0.002 TRP D 75 HIS 0.003 0.001 HIS D 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 ( 9932) covalent geometry : angle 0.57411 / 0.30 (13524) SS BOND : bond 0.00516 / 0.26 ( 4) SS BOND : angle 1.03437 / 0.60 ( 8) hydrogen bonds : bond 0.06001 / 3.89 ( 438) hydrogen bonds : angle 5.23038 / 3.70 ( 1296) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 295 time to evaluate : 0.466 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.8623 (tptt) cc_final: 0.8341 (tptt) REVERT: A 184 LYS cc_start: 0.8650 (tptp) cc_final: 0.8236 (tptt) REVERT: A 203 ARG cc_start: 0.7883 (mtp-110) cc_final: 0.7526 (mtp-110) REVERT: A 224 PHE cc_start: 0.8022 (m-80) cc_final: 0.7779 (m-80) REVERT: A 268 VAL cc_start: 0.8797 (p) cc_final: 0.8579 (m) REVERT: A 289 LEU cc_start: 0.8995 (mt) cc_final: 0.8743 (mm) REVERT: B 23 LYS cc_start: 0.8628 (tptt) cc_final: 0.8394 (tptt) REVERT: B 56 MET cc_start: 0.7322 (tpp) cc_final: 0.7122 (tpp) REVERT: B 181 MET cc_start: 0.5545 (mtp) cc_final: 0.5315 (mtp) REVERT: B 184 LYS cc_start: 0.8688 (tptp) cc_final: 0.8225 (tptt) REVERT: B 203 ARG cc_start: 0.7863 (mtp-110) cc_final: 0.7620 (mtp-110) REVERT: B 239 PHE cc_start: 0.8025 (p90) cc_final: 0.7823 (p90) REVERT: B 275 GLN cc_start: 0.7911 (mm110) cc_final: 0.7293 (mm110) REVERT: B 284 ARG cc_start: 0.5314 (tpt170) cc_final: 0.4379 (tpp80) REVERT: B 288 TYR cc_start: 0.7326 (m-80) cc_final: 0.7038 (m-80) REVERT: B 289 LEU cc_start: 0.8991 (mt) cc_final: 0.8748 (mm) REVERT: C 23 LYS cc_start: 0.8617 (tptt) cc_final: 0.8382 (tptt) REVERT: C 56 MET cc_start: 0.7300 (tpp) cc_final: 0.7088 (tpp) REVERT: C 81 MET cc_start: 0.7464 (mtp) cc_final: 0.7144 (mtp) REVERT: C 184 LYS cc_start: 0.8607 (tptp) cc_final: 0.8175 (tptt) REVERT: C 186 ASN cc_start: 0.6762 (m-40) cc_final: 0.6175 (m-40) REVERT: C 224 PHE cc_start: 0.8053 (m-80) cc_final: 0.7780 (m-80) REVERT: C 245 HIS cc_start: 0.6971 (t70) cc_final: 0.6750 (t70) REVERT: C 268 VAL cc_start: 0.8769 (p) cc_final: 0.8509 (m) REVERT: C 275 GLN cc_start: 0.7861 (mm110) cc_final: 0.7249 (mm110) REVERT: C 284 ARG cc_start: 0.5150 (tpt170) cc_final: 0.4157 (tpp80) REVERT: C 289 LEU cc_start: 0.9007 (mt) cc_final: 0.8761 (mm) REVERT: D 23 LYS cc_start: 0.8659 (tptt) cc_final: 0.8425 (tptt) REVERT: D 81 MET cc_start: 0.7505 (mtp) cc_final: 0.7189 (mtp) REVERT: D 224 PHE cc_start: 0.8041 (m-80) cc_final: 0.7748 (m-80) REVERT: D 275 GLN cc_start: 0.7678 (mm110) cc_final: 0.7282 (mm110) REVERT: D 284 ARG cc_start: 0.5261 (tpt170) cc_final: 0.4311 (tpp80) REVERT: D 289 LEU cc_start: 0.8925 (mt) cc_final: 0.8713 (mm) outliers start: 9 outliers final: 5 residues processed: 296 average time/residue: 0.1907 time to fit residues: 78.7848 Evaluate side-chains 295 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 290 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain D residue 173 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 29 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 chunk 87 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 41 optimal weight: 0.4980 chunk 107 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.186063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.147001 restraints weight = 42158.998| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.82 r_work: 0.3621 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9936 Z= 0.179 Angle : 0.553 4.998 13532 Z= 0.287 Chirality : 0.041 0.137 1532 Planarity : 0.005 0.052 1656 Dihedral : 7.460 85.727 1563 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.54 % Allowed : 11.87 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.26), residues: 1156 helix: 1.08 (0.25), residues: 380 sheet: -0.62 (0.32), residues: 248 loop : 0.46 (0.32), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 203 TYR 0.011 0.002 TYR B 288 PHE 0.022 0.002 PHE C 270 TRP 0.008 0.001 TRP D 55 HIS 0.003 0.001 HIS D 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 ( 9932) covalent geometry : angle 0.55284 / 0.29 (13524) SS BOND : bond 0.00456 / 0.23 ( 4) SS BOND : angle 1.05289 / 0.60 ( 8) hydrogen bonds : bond 0.05627 / 3.64 ( 438) hydrogen bonds : angle 4.87879 / 3.47 ( 1296) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 300 time to evaluate : 0.485 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: symmetry clash 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: symmetry clash 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: symmetry clash REVERT: A 23 LYS cc_start: 0.8661 (tptt) cc_final: 0.8332 (tptt) REVERT: A 184 LYS cc_start: 0.8668 (tptp) cc_final: 0.8259 (tptt) REVERT: A 186 ASN cc_start: 0.6998 (m-40) cc_final: 0.6395 (m-40) REVERT: A 224 PHE cc_start: 0.7968 (m-80) cc_final: 0.7758 (m-80) REVERT: A 268 VAL cc_start: 0.8808 (p) cc_final: 0.8585 (m) REVERT: A 284 ARG cc_start: 0.5497 (OUTLIER) cc_final: 0.4953 (ttt90) REVERT: A 289 LEU cc_start: 0.9008 (mt) cc_final: 0.8745 (mm) REVERT: A 294 MET cc_start: 0.7475 (mtp) cc_final: 0.7128 (mtp) REVERT: B 23 LYS cc_start: 0.8643 (tptt) cc_final: 0.8325 (tptt) REVERT: B 184 LYS cc_start: 0.8701 (tptp) cc_final: 0.8289 (tptt) REVERT: B 203 ARG cc_start: 0.7963 (mtp-110) cc_final: 0.7609 (mtp-110) REVERT: B 239 PHE cc_start: 0.8034 (p90) cc_final: 0.7807 (p90) REVERT: B 284 ARG cc_start: 0.5409 (OUTLIER) cc_final: 0.4825 (ttt90) REVERT: B 289 LEU cc_start: 0.9013 (mt) cc_final: 0.8761 (mm) REVERT: B 294 MET cc_start: 0.7505 (mtp) cc_final: 0.7187 (mtp) REVERT: C 23 LYS cc_start: 0.8627 (tptt) cc_final: 0.8329 (tptt) REVERT: C 81 MET cc_start: 0.7414 (mtp) cc_final: 0.7098 (mtp) REVERT: C 186 ASN cc_start: 0.6813 (m-40) cc_final: 0.6320 (m-40) REVERT: C 224 PHE cc_start: 0.8042 (m-80) cc_final: 0.7768 (m-80) REVERT: C 268 VAL cc_start: 0.8779 (p) cc_final: 0.8544 (m) REVERT: C 289 LEU cc_start: 0.9014 (mt) cc_final: 0.8760 (mm) REVERT: C 294 MET cc_start: 0.7556 (mtp) cc_final: 0.7217 (mtp) REVERT: D 23 LYS cc_start: 0.8664 (tptt) cc_final: 0.8325 (tptt) REVERT: D 81 MET cc_start: 0.7472 (mtp) cc_final: 0.7160 (mtp) REVERT: D 186 ASN cc_start: 0.6768 (m-40) cc_final: 0.6267 (m-40) REVERT: D 224 PHE cc_start: 0.7998 (m-80) cc_final: 0.7756 (m-80) REVERT: D 289 LEU cc_start: 0.8961 (mt) cc_final: 0.8730 (mm) outliers start: 16 outliers final: 8 residues processed: 302 average time/residue: 0.2048 time to fit residues: 85.0576 Evaluate side-chains 309 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 299 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 284 ARG Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 284 ARG Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 284 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 103 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 39 optimal weight: 0.0670 chunk 111 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 overall best weight: 1.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.186594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.147392 restraints weight = 42251.612| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.80 r_work: 0.3648 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 9936 Z= 0.157 Angle : 0.525 4.373 13532 Z= 0.271 Chirality : 0.040 0.133 1532 Planarity : 0.005 0.052 1656 Dihedral : 7.435 88.407 1563 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.74 % Allowed : 12.84 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.26), residues: 1156 helix: 1.31 (0.26), residues: 380 sheet: -0.76 (0.31), residues: 240 loop : 0.37 (0.31), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 203 TYR 0.011 0.002 TYR B 288 PHE 0.021 0.002 PHE A 270 TRP 0.006 0.001 TRP C 55 HIS 0.003 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 9932) covalent geometry : angle 0.52504 / 0.27 (13524) SS BOND : bond 0.00402 / 0.20 ( 4) SS BOND : angle 0.92329 / 0.54 ( 8) hydrogen bonds : bond 0.05216 / 3.38 ( 438) hydrogen bonds : angle 4.64504 / 3.31 ( 1296) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 298 time to evaluate : 0.313 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: symmetry clash 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: 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 23 LYS cc_start: 0.8689 (tptt) cc_final: 0.8316 (tptt) REVERT: A 186 ASN cc_start: 0.7038 (m-40) cc_final: 0.6586 (m-40) REVERT: A 268 VAL cc_start: 0.8793 (p) cc_final: 0.8565 (m) REVERT: A 289 LEU cc_start: 0.9009 (mt) cc_final: 0.8751 (mm) REVERT: A 294 MET cc_start: 0.7463 (mtp) cc_final: 0.7136 (mtp) REVERT: B 23 LYS cc_start: 0.8660 (tptt) cc_final: 0.8295 (tptt) REVERT: B 184 LYS cc_start: 0.8650 (tptp) cc_final: 0.8181 (tptt) REVERT: B 239 PHE cc_start: 0.8032 (p90) cc_final: 0.7785 (p90) REVERT: B 289 LEU cc_start: 0.9021 (mt) cc_final: 0.8776 (mm) REVERT: B 294 MET cc_start: 0.7521 (mtp) cc_final: 0.7188 (mtp) REVERT: C 23 LYS cc_start: 0.8630 (tptt) cc_final: 0.8291 (tptt) REVERT: C 81 MET cc_start: 0.7430 (mtp) cc_final: 0.7128 (mtp) REVERT: C 186 ASN cc_start: 0.6813 (m-40) cc_final: 0.6393 (m-40) REVERT: C 224 PHE cc_start: 0.7974 (m-80) cc_final: 0.7755 (m-80) REVERT: C 268 VAL cc_start: 0.8767 (p) cc_final: 0.8534 (m) REVERT: C 289 LEU cc_start: 0.9027 (mt) cc_final: 0.8781 (mm) REVERT: C 294 MET cc_start: 0.7547 (mtp) cc_final: 0.7231 (mtp) REVERT: D 23 LYS cc_start: 0.8693 (tptt) cc_final: 0.8358 (tptt) REVERT: D 186 ASN cc_start: 0.6840 (m-40) cc_final: 0.6361 (m-40) REVERT: D 268 VAL cc_start: 0.8807 (p) cc_final: 0.8602 (m) REVERT: D 275 GLN cc_start: 0.7772 (mm110) cc_final: 0.7136 (mm110) REVERT: D 289 LEU cc_start: 0.8987 (mt) cc_final: 0.8747 (mm) outliers start: 18 outliers final: 17 residues processed: 307 average time/residue: 0.2032 time to fit residues: 86.7070 Evaluate side-chains 312 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 295 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 244 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 66 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 78 optimal weight: 0.2980 chunk 84 optimal weight: 5.9990 chunk 2 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 180 HIS ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.186958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.147785 restraints weight = 42340.561| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.82 r_work: 0.3649 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9936 Z= 0.145 Angle : 0.522 5.073 13532 Z= 0.267 Chirality : 0.040 0.133 1532 Planarity : 0.004 0.052 1656 Dihedral : 7.182 83.278 1563 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.12 % Allowed : 13.42 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.26), residues: 1156 helix: 1.44 (0.26), residues: 380 sheet: -0.64 (0.32), residues: 244 loop : 0.43 (0.31), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 203 TYR 0.010 0.001 TYR D 288 PHE 0.022 0.002 PHE D 270 TRP 0.007 0.001 TRP A 55 HIS 0.003 0.001 HIS B 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 9932) covalent geometry : angle 0.52137 / 0.27 (13524) SS BOND : bond 0.00369 / 0.19 ( 4) SS BOND : angle 0.84032 / 0.49 ( 8) hydrogen bonds : bond 0.04973 / 3.23 ( 438) hydrogen bonds : angle 4.49122 / 3.21 ( 1296) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 293 time to evaluate : 0.353 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: symmetry clash 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: symmetry clash 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: symmetry clash REVERT: A 23 LYS cc_start: 0.8688 (tptt) cc_final: 0.8289 (tptt) REVERT: A 186 ASN cc_start: 0.6977 (m-40) cc_final: 0.6571 (m-40) REVERT: A 268 VAL cc_start: 0.8767 (p) cc_final: 0.8537 (m) REVERT: A 289 LEU cc_start: 0.9034 (mt) cc_final: 0.8771 (mm) REVERT: A 294 MET cc_start: 0.7477 (mtp) cc_final: 0.7128 (mtp) REVERT: B 23 LYS cc_start: 0.8695 (tptt) cc_final: 0.8291 (tptt) REVERT: B 239 PHE cc_start: 0.8035 (p90) cc_final: 0.7790 (p90) REVERT: B 275 GLN cc_start: 0.7871 (mm110) cc_final: 0.7280 (mm110) REVERT: B 289 LEU cc_start: 0.9015 (mt) cc_final: 0.8768 (mm) REVERT: B 294 MET cc_start: 0.7503 (mtp) cc_final: 0.7181 (mtp) REVERT: C 23 LYS cc_start: 0.8626 (tptt) cc_final: 0.8297 (tptt) REVERT: C 186 ASN cc_start: 0.6931 (m-40) cc_final: 0.6458 (m-40) REVERT: C 268 VAL cc_start: 0.8771 (p) cc_final: 0.8520 (m) REVERT: C 275 GLN cc_start: 0.7848 (mm110) cc_final: 0.7183 (mm110) REVERT: C 289 LEU cc_start: 0.9026 (mt) cc_final: 0.8775 (mm) REVERT: C 294 MET cc_start: 0.7514 (mtp) cc_final: 0.7181 (mtp) REVERT: D 23 LYS cc_start: 0.8714 (tptt) cc_final: 0.8308 (tptt) REVERT: D 186 ASN cc_start: 0.6865 (m-40) cc_final: 0.6433 (m-40) REVERT: D 275 GLN cc_start: 0.7777 (mm110) cc_final: 0.7106 (mm110) REVERT: D 289 LEU cc_start: 0.8991 (mt) cc_final: 0.8738 (mm) outliers start: 22 outliers final: 20 residues processed: 300 average time/residue: 0.1952 time to fit residues: 80.6489 Evaluate side-chains 311 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 291 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 284 ARG Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 284 ARG Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 244 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 79 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 85 optimal weight: 20.0000 chunk 83 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.186866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.147636 restraints weight = 41893.162| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.79 r_work: 0.3631 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9936 Z= 0.148 Angle : 0.514 4.292 13532 Z= 0.262 Chirality : 0.040 0.127 1532 Planarity : 0.004 0.051 1656 Dihedral : 6.925 76.682 1563 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.32 % Allowed : 14.48 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.26), residues: 1156 helix: 1.51 (0.26), residues: 380 sheet: -0.61 (0.32), residues: 244 loop : 0.41 (0.31), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 203 TYR 0.009 0.001 TYR A 288 PHE 0.019 0.002 PHE D 270 TRP 0.004 0.001 TRP A 55 HIS 0.003 0.001 HIS D 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 9932) covalent geometry : angle 0.51351 / 0.26 (13524) SS BOND : bond 0.00376 / 0.19 ( 4) SS BOND : angle 0.86077 / 0.50 ( 8) hydrogen bonds : bond 0.04942 / 3.20 ( 438) hydrogen bonds : angle 4.42619 / 3.17 ( 1296) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 291 time to evaluate : 0.357 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: symmetry clash 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: symmetry clash 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 23 LYS cc_start: 0.8735 (tptt) cc_final: 0.8314 (tptt) REVERT: A 186 ASN cc_start: 0.7050 (m-40) cc_final: 0.6701 (m-40) REVERT: A 268 VAL cc_start: 0.8774 (p) cc_final: 0.8531 (m) REVERT: A 289 LEU cc_start: 0.9041 (mt) cc_final: 0.8767 (mm) REVERT: A 294 MET cc_start: 0.7511 (mtp) cc_final: 0.7231 (mtp) REVERT: B 239 PHE cc_start: 0.8018 (p90) cc_final: 0.7764 (p90) REVERT: B 275 GLN cc_start: 0.7938 (mm110) cc_final: 0.7290 (mm110) REVERT: B 289 LEU cc_start: 0.9022 (mt) cc_final: 0.8786 (mm) REVERT: B 294 MET cc_start: 0.7569 (mtp) cc_final: 0.7275 (mtp) REVERT: C 23 LYS cc_start: 0.8692 (tptt) cc_final: 0.8302 (tptt) REVERT: C 186 ASN cc_start: 0.6951 (m-40) cc_final: 0.6570 (m-40) REVERT: C 268 VAL cc_start: 0.8751 (p) cc_final: 0.8508 (m) REVERT: C 289 LEU cc_start: 0.9026 (mt) cc_final: 0.8770 (mm) REVERT: C 294 MET cc_start: 0.7575 (mtp) cc_final: 0.7233 (mtp) REVERT: D 186 ASN cc_start: 0.6887 (m-40) cc_final: 0.6522 (m-40) REVERT: D 275 GLN cc_start: 0.7801 (mm110) cc_final: 0.7095 (mm110) REVERT: D 289 LEU cc_start: 0.9006 (mt) cc_final: 0.8770 (mt) REVERT: D 294 MET cc_start: 0.7508 (mtp) cc_final: 0.7237 (mtp) outliers start: 24 outliers final: 20 residues processed: 299 average time/residue: 0.1995 time to fit residues: 82.4279 Evaluate side-chains 308 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 288 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 284 ARG Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 284 ARG Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 244 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 18 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 92 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.184976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.145243 restraints weight = 42031.488| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.81 r_work: 0.3611 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9936 Z= 0.214 Angle : 0.552 4.074 13532 Z= 0.288 Chirality : 0.041 0.125 1532 Planarity : 0.005 0.050 1656 Dihedral : 6.982 76.239 1563 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.12 % Allowed : 14.67 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.26), residues: 1156 helix: 1.47 (0.26), residues: 352 sheet: -1.12 (0.29), residues: 304 loop : 0.44 (0.33), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 203 TYR 0.012 0.002 TYR C 218 PHE 0.019 0.002 PHE D 270 TRP 0.007 0.002 TRP D 53 HIS 0.003 0.001 HIS C 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.21 ( 9932) covalent geometry : angle 0.55135 / 0.29 (13524) SS BOND : bond 0.00501 / 0.25 ( 4) SS BOND : angle 1.24446 / 0.73 ( 8) hydrogen bonds : bond 0.05802 / 3.76 ( 438) hydrogen bonds : angle 4.61037 / 3.30 ( 1296) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 292 time to evaluate : 0.282 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 ASN cc_start: 0.7100 (m-40) cc_final: 0.6841 (m-40) REVERT: A 268 VAL cc_start: 0.8791 (p) cc_final: 0.8544 (m) REVERT: A 289 LEU cc_start: 0.9078 (mt) cc_final: 0.8821 (mm) REVERT: A 294 MET cc_start: 0.7593 (mtp) cc_final: 0.7322 (mtp) REVERT: B 20 MET cc_start: 0.6886 (mmm) cc_final: 0.6680 (tmm) REVERT: B 23 LYS cc_start: 0.8734 (tptt) cc_final: 0.8325 (tptt) REVERT: B 289 LEU cc_start: 0.9066 (mt) cc_final: 0.8815 (mm) REVERT: B 294 MET cc_start: 0.7615 (mtp) cc_final: 0.7373 (mtp) REVERT: C 23 LYS cc_start: 0.8680 (tptt) cc_final: 0.8300 (tptt) REVERT: C 186 ASN cc_start: 0.7072 (m-40) cc_final: 0.6806 (m-40) REVERT: C 268 VAL cc_start: 0.8741 (p) cc_final: 0.8477 (m) REVERT: C 284 ARG cc_start: 0.5576 (OUTLIER) cc_final: 0.4915 (ttt90) REVERT: C 289 LEU cc_start: 0.9082 (mt) cc_final: 0.8833 (mm) REVERT: C 294 MET cc_start: 0.7622 (mtp) cc_final: 0.7362 (mtp) REVERT: D 186 ASN cc_start: 0.7032 (m-40) cc_final: 0.6806 (m-40) REVERT: D 275 GLN cc_start: 0.7801 (mm110) cc_final: 0.7181 (mm110) REVERT: D 289 LEU cc_start: 0.9042 (mt) cc_final: 0.8802 (mm) REVERT: D 294 MET cc_start: 0.7590 (mtp) cc_final: 0.7337 (mtp) outliers start: 22 outliers final: 21 residues processed: 302 average time/residue: 0.1837 time to fit residues: 76.8208 Evaluate side-chains 313 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 291 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 284 ARG Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 284 ARG Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 284 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 73 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 56 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.185498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.145649 restraints weight = 41801.700| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.82 r_work: 0.3619 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9936 Z= 0.193 Angle : 0.541 5.381 13532 Z= 0.279 Chirality : 0.041 0.127 1532 Planarity : 0.005 0.053 1656 Dihedral : 6.781 81.512 1563 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.32 % Allowed : 15.25 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.27), residues: 1156 helix: 1.58 (0.26), residues: 352 sheet: -1.15 (0.29), residues: 304 loop : 0.43 (0.33), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 203 TYR 0.010 0.001 TYR A 288 PHE 0.016 0.002 PHE D 270 TRP 0.006 0.002 TRP A 53 HIS 0.003 0.001 HIS D 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 ( 9932) covalent geometry : angle 0.54023 / 0.28 (13524) SS BOND : bond 0.00431 / 0.22 ( 4) SS BOND : angle 1.06870 / 0.63 ( 8) hydrogen bonds : bond 0.05385 / 3.49 ( 438) hydrogen bonds : angle 4.49900 / 3.22 ( 1296) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 288 time to evaluate : 0.499 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.8736 (tptt) cc_final: 0.8341 (tptt) REVERT: A 186 ASN cc_start: 0.7072 (m-40) cc_final: 0.6860 (m-40) REVERT: A 289 LEU cc_start: 0.9081 (mt) cc_final: 0.8802 (mm) REVERT: A 294 MET cc_start: 0.7568 (mtp) cc_final: 0.7303 (mtp) REVERT: B 284 ARG cc_start: 0.5485 (OUTLIER) cc_final: 0.4925 (ttt90) REVERT: B 289 LEU cc_start: 0.9065 (mt) cc_final: 0.8831 (mm) REVERT: B 294 MET cc_start: 0.7610 (mtp) cc_final: 0.7362 (mtp) REVERT: C 23 LYS cc_start: 0.8728 (tptt) cc_final: 0.8332 (tptt) REVERT: C 275 GLN cc_start: 0.7880 (mm110) cc_final: 0.7299 (mm110) REVERT: C 284 ARG cc_start: 0.5535 (OUTLIER) cc_final: 0.4906 (ttt90) REVERT: C 289 LEU cc_start: 0.9080 (mt) cc_final: 0.8833 (mm) REVERT: C 294 MET cc_start: 0.7571 (mtp) cc_final: 0.7313 (mtp) REVERT: D 186 ASN cc_start: 0.7032 (m-40) cc_final: 0.6816 (m-40) REVERT: D 275 GLN cc_start: 0.7811 (mm110) cc_final: 0.7183 (mm110) REVERT: D 289 LEU cc_start: 0.9039 (mt) cc_final: 0.8792 (mm) REVERT: D 294 MET cc_start: 0.7637 (mtp) cc_final: 0.7372 (mtp) outliers start: 24 outliers final: 19 residues processed: 303 average time/residue: 0.1940 time to fit residues: 81.4637 Evaluate side-chains 309 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 288 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 284 ARG Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 284 ARG Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 244 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 83 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 245 HIS D 245 HIS ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.182037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.142371 restraints weight = 41938.737| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.78 r_work: 0.3554 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 9936 Z= 0.289 Angle : 0.610 4.976 13532 Z= 0.320 Chirality : 0.043 0.147 1532 Planarity : 0.005 0.054 1656 Dihedral : 6.925 85.654 1563 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.41 % Allowed : 15.44 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.26), residues: 1156 helix: 1.12 (0.26), residues: 352 sheet: -1.22 (0.29), residues: 304 loop : 0.18 (0.32), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 203 TYR 0.015 0.002 TYR A 288 PHE 0.025 0.002 PHE A 156 TRP 0.010 0.003 TRP D 53 HIS 0.006 0.001 HIS D 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00663 / 0.29 ( 9932) covalent geometry : angle 0.60918 / 0.32 (13524) SS BOND : bond 0.00646 / 0.32 ( 4) SS BOND : angle 1.52646 / 0.90 ( 8) hydrogen bonds : bond 0.06498 / 4.22 ( 438) hydrogen bonds : angle 4.80290 / 3.45 ( 1296) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 296 time to evaluate : 0.481 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.8778 (tptt) cc_final: 0.8372 (tptt) REVERT: A 186 ASN cc_start: 0.7265 (m-40) cc_final: 0.7015 (m-40) REVERT: A 289 LEU cc_start: 0.9109 (mt) cc_final: 0.8775 (mt) REVERT: A 294 MET cc_start: 0.7679 (mtp) cc_final: 0.7436 (mtp) REVERT: B 23 LYS cc_start: 0.8741 (tptt) cc_final: 0.8376 (tptt) REVERT: B 284 ARG cc_start: 0.5631 (OUTLIER) cc_final: 0.4965 (ttt90) REVERT: B 289 LEU cc_start: 0.9077 (mt) cc_final: 0.8730 (mt) REVERT: C 23 LYS cc_start: 0.8774 (tptt) cc_final: 0.8428 (tptt) REVERT: C 186 ASN cc_start: 0.7265 (m-40) cc_final: 0.7053 (m-40) REVERT: C 275 GLN cc_start: 0.7933 (mm110) cc_final: 0.7326 (mm110) REVERT: C 284 ARG cc_start: 0.5600 (OUTLIER) cc_final: 0.4932 (ttt90) REVERT: C 289 LEU cc_start: 0.9090 (mt) cc_final: 0.8750 (mt) REVERT: C 294 MET cc_start: 0.7712 (mtp) cc_final: 0.7477 (mtp) REVERT: D 186 ASN cc_start: 0.7189 (m-40) cc_final: 0.6989 (m-40) REVERT: D 275 GLN cc_start: 0.7858 (mm110) cc_final: 0.7180 (mm110) REVERT: D 289 LEU cc_start: 0.9081 (mt) cc_final: 0.8845 (mm) outliers start: 25 outliers final: 21 residues processed: 311 average time/residue: 0.2127 time to fit residues: 90.8434 Evaluate side-chains 318 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 295 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 284 ARG Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 284 ARG Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 284 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 76 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 74 optimal weight: 0.1980 chunk 23 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.186465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.146848 restraints weight = 41892.952| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.83 r_work: 0.3634 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9936 Z= 0.126 Angle : 0.544 5.442 13532 Z= 0.275 Chirality : 0.040 0.126 1532 Planarity : 0.005 0.053 1656 Dihedral : 6.532 85.120 1563 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.35 % Allowed : 16.41 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.27), residues: 1156 helix: 1.89 (0.27), residues: 352 sheet: -1.18 (0.28), residues: 304 loop : 0.38 (0.34), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 203 TYR 0.009 0.001 TYR C 288 PHE 0.018 0.002 PHE C 270 TRP 0.008 0.001 TRP D 53 HIS 0.003 0.001 HIS C 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 9932) covalent geometry : angle 0.54353 / 0.28 (13524) SS BOND : bond 0.00234 / 0.12 ( 4) SS BOND : angle 0.57729 / 0.33 ( 8) hydrogen bonds : bond 0.04470 / 2.91 ( 438) hydrogen bonds : angle 4.28915 / 3.08 ( 1296) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 286 time to evaluate : 0.487 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 ASN cc_start: 0.7052 (m-40) cc_final: 0.6843 (m-40) REVERT: A 289 LEU cc_start: 0.9078 (mt) cc_final: 0.8777 (mt) REVERT: A 294 MET cc_start: 0.7649 (mtp) cc_final: 0.7375 (mtp) REVERT: B 23 LYS cc_start: 0.8776 (tptt) cc_final: 0.8396 (tptt) REVERT: B 186 ASN cc_start: 0.6955 (m-40) cc_final: 0.6546 (m-40) REVERT: B 289 LEU cc_start: 0.9057 (mt) cc_final: 0.8807 (mm) REVERT: B 294 MET cc_start: 0.7708 (mtp) cc_final: 0.7448 (mtp) REVERT: C 23 LYS cc_start: 0.8781 (tptt) cc_final: 0.8431 (tptt) REVERT: C 186 ASN cc_start: 0.7103 (m-40) cc_final: 0.6865 (m-40) REVERT: C 275 GLN cc_start: 0.7937 (mm110) cc_final: 0.7342 (mm110) REVERT: C 289 LEU cc_start: 0.9065 (mt) cc_final: 0.8815 (mm) REVERT: C 294 MET cc_start: 0.7664 (mtp) cc_final: 0.7385 (mtp) REVERT: D 275 GLN cc_start: 0.7791 (mm110) cc_final: 0.7191 (mm110) REVERT: D 294 MET cc_start: 0.7756 (mtp) cc_final: 0.7454 (mtp) outliers start: 14 outliers final: 14 residues processed: 298 average time/residue: 0.2182 time to fit residues: 89.3755 Evaluate side-chains 298 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 284 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 205 SER Chi-restraints excluded: chain D residue 244 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 13 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 64 optimal weight: 0.0870 chunk 72 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 245 HIS ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.185105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.145233 restraints weight = 42250.408| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.82 r_work: 0.3625 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9936 Z= 0.137 Angle : 0.539 9.627 13532 Z= 0.272 Chirality : 0.040 0.125 1532 Planarity : 0.005 0.054 1656 Dihedral : 6.435 85.737 1563 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.54 % Allowed : 16.70 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.27), residues: 1156 helix: 2.02 (0.26), residues: 352 sheet: -1.17 (0.29), residues: 304 loop : 0.31 (0.33), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 203 TYR 0.008 0.001 TYR A 288 PHE 0.018 0.002 PHE D 270 TRP 0.009 0.001 TRP D 53 HIS 0.003 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 9932) covalent geometry : angle 0.53931 / 0.27 (13524) SS BOND : bond 0.00374 / 0.19 ( 4) SS BOND : angle 0.72606 / 0.42 ( 8) hydrogen bonds : bond 0.04684 / 3.04 ( 438) hydrogen bonds : angle 4.27428 / 3.07 ( 1296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4294.79 seconds wall clock time: 73 minutes 22.21 seconds (4402.21 seconds total)