Starting phenix.real_space_refine on Sat Jul 4 09:22:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i5m_35195/07_2026/8i5m_35195_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i5m_35195/07_2026/8i5m_35195.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i5m_35195/07_2026/8i5m_35195.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i5m_35195/07_2026/8i5m_35195.map" model { file = "/net/cci-nas-00/data/ceres_data/8i5m_35195/07_2026/8i5m_35195_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i5m_35195/07_2026/8i5m_35195_trim.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 36 5.16 5 C 6484 2.51 5 N 1648 2.21 5 O 1840 1.98 5 H 10060 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 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: 20080 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 4983 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 11, 'TRANS': 298} Chain: "B" Number of atoms: 4983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 4983 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 11, 'TRANS': 298} Chain: "C" Number of atoms: 4983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 4983 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 11, 'TRANS': 298} Chain: "D" Number of atoms: 4983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 4983 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 11, 'TRANS': 298} Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Time building chain proxies: 2.91, per 1000 atoms: 0.14 Number of scatterers: 20080 At special positions: 0 Unit cell: (98.358, 98.358, 114.582, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 12 15.00 O 1840 8.00 N 1648 7.00 C 6484 6.00 H 10060 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 140 " distance=2.03 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 140 " distance=2.03 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 140 " distance=2.03 Simple disulfide: pdb=" SG CYS D 108 " - pdb=" SG CYS D 140 " 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: 1.70 Conformation dependent library (CDL) restraints added in 621.2 milliseconds 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2336 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 28 sheets defined 33.5% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 54 through 62 Processing helix chain 'A' and resid 63 through 93 Processing helix chain 'A' and resid 114 through 127 Processing helix chain 'A' and resid 140 through 171 removed outlier: 3.694A pdb=" N ILE A 144 " --> pdb=" O CYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 removed outlier: 3.675A pdb=" N GLU A 177 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 54 through 62 Processing helix chain 'B' and resid 63 through 93 Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'B' and resid 140 through 171 removed outlier: 3.694A pdb=" N ILE B 144 " --> pdb=" O CYS B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 removed outlier: 3.676A pdb=" N GLU B 177 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 330 No H-bonds generated for 'chain 'B' and resid 328 through 330' Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 54 through 62 Processing helix chain 'C' and resid 63 through 93 Processing helix chain 'C' and resid 114 through 127 Processing helix chain 'C' and resid 140 through 171 removed outlier: 3.694A pdb=" N ILE C 144 " --> pdb=" O CYS C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 177 removed outlier: 3.676A pdb=" N GLU C 177 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 330 No H-bonds generated for 'chain 'C' and resid 328 through 330' Processing helix chain 'D' and resid 46 through 54 Processing helix chain 'D' and resid 54 through 62 Processing helix chain 'D' and resid 63 through 93 Processing helix chain 'D' and resid 114 through 127 Processing helix chain 'D' and resid 140 through 171 removed outlier: 3.694A pdb=" N ILE D 144 " --> pdb=" O CYS D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 177 removed outlier: 3.676A pdb=" N GLU D 177 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 330 No H-bonds generated for 'chain 'D' and resid 328 through 330' Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 42 Processing sheet with id=AA2, first strand: chain 'A' and resid 179 through 181 Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 181 Processing sheet with id=AA4, first strand: chain 'A' and resid 233 through 237 removed outlier: 6.978A pdb=" N ILE A 209 " --> pdb=" O PHE A 248 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N PHE A 248 " --> pdb=" O ILE A 209 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 233 through 237 removed outlier: 4.116A pdb=" N CYS A 211 " --> pdb=" O SER A 284 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N SER A 284 " --> pdb=" O CYS A 211 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL A 213 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE A 282 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLY A 215 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL A 280 " --> pdb=" O GLY A 215 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU A 217 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLU A 278 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 221 through 222 removed outlier: 3.918A pdb=" N HIS A 221 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A 230 " --> pdb=" O HIS A 221 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 309 through 311 Processing sheet with id=AA8, first strand: chain 'A' and resid 315 through 316 removed outlier: 6.487A pdb=" N TYR A 323 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N GLU B 42 " --> pdb=" O TYR A 323 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ALA A 325 " --> pdb=" O GLU B 42 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 179 through 181 Processing sheet with id=AB1, first strand: chain 'B' and resid 179 through 181 Processing sheet with id=AB2, first strand: chain 'B' and resid 233 through 237 removed outlier: 6.979A pdb=" N ILE B 209 " --> pdb=" O PHE B 248 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE B 248 " --> pdb=" O ILE B 209 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 233 through 237 removed outlier: 4.116A pdb=" N CYS B 211 " --> pdb=" O SER B 284 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N SER B 284 " --> pdb=" O CYS B 211 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL B 213 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE B 282 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLY B 215 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL B 280 " --> pdb=" O GLY B 215 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU B 217 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLU B 278 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 221 through 222 removed outlier: 3.917A pdb=" N HIS B 221 " --> pdb=" O ARG B 230 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG B 230 " --> pdb=" O HIS B 221 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 309 through 311 Processing sheet with id=AB6, first strand: chain 'B' and resid 315 through 316 removed outlier: 6.401A pdb=" N TYR B 323 " --> pdb=" O ARG C 40 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N GLU C 42 " --> pdb=" O TYR B 323 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ALA B 325 " --> pdb=" O GLU C 42 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 179 through 181 Processing sheet with id=AB8, first strand: chain 'C' and resid 179 through 181 Processing sheet with id=AB9, first strand: chain 'C' and resid 233 through 237 removed outlier: 6.979A pdb=" N ILE C 209 " --> pdb=" O PHE C 248 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE C 248 " --> pdb=" O ILE C 209 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 233 through 237 removed outlier: 4.116A pdb=" N CYS C 211 " --> pdb=" O SER C 284 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N SER C 284 " --> pdb=" O CYS C 211 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL C 213 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE C 282 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLY C 215 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL C 280 " --> pdb=" O GLY C 215 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU C 217 " --> pdb=" O GLU C 278 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLU C 278 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 221 through 222 removed outlier: 3.917A pdb=" N HIS C 221 " --> pdb=" O ARG C 230 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG C 230 " --> pdb=" O HIS C 221 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 309 through 311 Processing sheet with id=AC4, first strand: chain 'C' and resid 315 through 316 removed outlier: 6.401A pdb=" N TYR C 323 " --> pdb=" O ARG D 40 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N GLU D 42 " --> pdb=" O TYR C 323 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ALA C 325 " --> pdb=" O GLU D 42 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 179 through 181 Processing sheet with id=AC6, first strand: chain 'D' and resid 179 through 181 Processing sheet with id=AC7, first strand: chain 'D' and resid 233 through 237 removed outlier: 6.979A pdb=" N ILE D 209 " --> pdb=" O PHE D 248 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE D 248 " --> pdb=" O ILE D 209 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 233 through 237 removed outlier: 4.116A pdb=" N CYS D 211 " --> pdb=" O SER D 284 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N SER D 284 " --> pdb=" O CYS D 211 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL D 213 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE D 282 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLY D 215 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL D 280 " --> pdb=" O GLY D 215 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU D 217 " --> pdb=" O GLU D 278 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLU D 278 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 221 through 222 removed outlier: 3.917A pdb=" N HIS D 221 " --> pdb=" O ARG D 230 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG D 230 " --> pdb=" O HIS D 221 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 309 through 311 471 hydrogen bonds defined for protein. 1341 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: 3.99 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.02: 10048 1.02 - 1.22: 20 1.22 - 1.41: 4203 1.41 - 1.61: 5969 1.61 - 1.80: 68 Bond restraints: 20308 Sorted by residual: bond pdb=" O51 PIO A 401 " pdb=" P5 PIO A 401 " ideal model delta sigma weight residual 1.528 1.456 0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" O51 PIO B 401 " pdb=" P5 PIO B 401 " ideal model delta sigma weight residual 1.528 1.456 0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" O51 PIO D 401 " pdb=" P5 PIO D 401 " ideal model delta sigma weight residual 1.528 1.456 0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" O51 PIO C 401 " pdb=" P5 PIO C 401 " ideal model delta sigma weight residual 1.528 1.456 0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" O43 PIO A 401 " pdb=" P4 PIO A 401 " ideal model delta sigma weight residual 1.529 1.458 0.071 2.00e-02 2.50e+03 1.27e+01 ... (remaining 20303 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.05: 36592 4.05 - 8.11: 68 8.11 - 12.16: 40 12.16 - 16.22: 8 16.22 - 20.27: 4 Bond angle restraints: 36712 Sorted by residual: angle pdb=" O11 PIO B 401 " pdb=" P1 PIO B 401 " pdb=" O12 PIO B 401 " ideal model delta sigma weight residual 121.09 100.82 20.27 3.00e+00 1.11e-01 4.57e+01 angle pdb=" O11 PIO C 401 " pdb=" P1 PIO C 401 " pdb=" O12 PIO C 401 " ideal model delta sigma weight residual 121.09 100.82 20.27 3.00e+00 1.11e-01 4.57e+01 angle pdb=" O11 PIO D 401 " pdb=" P1 PIO D 401 " pdb=" O12 PIO D 401 " ideal model delta sigma weight residual 121.09 100.82 20.27 3.00e+00 1.11e-01 4.57e+01 angle pdb=" O11 PIO A 401 " pdb=" P1 PIO A 401 " pdb=" O12 PIO A 401 " ideal model delta sigma weight residual 121.09 100.85 20.24 3.00e+00 1.11e-01 4.55e+01 angle pdb=" O4 PIO B 401 " pdb=" P4 PIO B 401 " pdb=" O41 PIO B 401 " ideal model delta sigma weight residual 101.33 114.24 -12.91 3.00e+00 1.11e-01 1.85e+01 ... (remaining 36707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.31: 8072 12.31 - 24.63: 1023 24.63 - 36.94: 181 36.94 - 49.26: 112 49.26 - 61.57: 92 Dihedral angle restraints: 9480 sinusoidal: 5112 harmonic: 4368 Sorted by residual: dihedral pdb=" CA THR B 223 " pdb=" C THR B 223 " pdb=" N LYS B 224 " pdb=" CA LYS B 224 " ideal model delta harmonic sigma weight residual -180.00 -151.32 -28.68 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA THR C 223 " pdb=" C THR C 223 " pdb=" N LYS C 224 " pdb=" CA LYS C 224 " ideal model delta harmonic sigma weight residual -180.00 -151.32 -28.68 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA THR D 223 " pdb=" C THR D 223 " pdb=" N LYS D 224 " pdb=" CA LYS D 224 " ideal model delta harmonic sigma weight residual 180.00 -151.32 -28.68 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 9477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 845 0.030 - 0.060: 453 0.060 - 0.089: 234 0.089 - 0.119: 107 0.119 - 0.149: 13 Chirality restraints: 1652 Sorted by residual: chirality pdb=" CA ILE A 198 " pdb=" N ILE A 198 " pdb=" C ILE A 198 " pdb=" CB ILE A 198 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.54e-01 chirality pdb=" CA ILE C 198 " pdb=" N ILE C 198 " pdb=" C ILE C 198 " pdb=" CB ILE C 198 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA ILE B 198 " pdb=" N ILE B 198 " pdb=" C ILE B 198 " pdb=" CB ILE B 198 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 ... (remaining 1649 not shown) Planarity restraints: 2900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 171 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO B 172 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 172 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 172 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 171 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO C 172 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 172 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 172 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 171 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO D 172 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 172 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 172 " -0.023 5.00e-02 4.00e+02 ... (remaining 2897 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1275 2.18 - 2.79: 42688 2.79 - 3.39: 52154 3.39 - 4.00: 70145 4.00 - 4.60: 109998 Nonbonded interactions: 276260 Sorted by model distance: nonbonded pdb=" HZ3 LYS B 216 " pdb=" OD1 ASN B 235 " model vdw 1.581 2.450 nonbonded pdb=" HZ3 LYS D 216 " pdb=" OD1 ASN D 235 " model vdw 1.583 2.450 nonbonded pdb=" HZ3 LYS C 216 " pdb=" OD1 ASN C 235 " model vdw 1.583 2.450 nonbonded pdb=" HZ3 LYS A 216 " pdb=" OD1 ASN A 235 " model vdw 1.583 2.450 nonbonded pdb=" HZ3 LYS A 33 " pdb=" OE1 GLU A 304 " model vdw 1.599 2.450 ... (remaining 276255 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.590 Find NCS groups from input model: 0.290 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: 0.010 Load rotamer database and sin/cos tables:5.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 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 : 0.012 0.072 10252 Z= 0.503 Angle : 1.057 20.272 13960 Z= 0.493 Chirality : 0.046 0.149 1652 Planarity : 0.004 0.043 1708 Dihedral : 11.548 61.574 3644 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -2.38 (0.21), residues: 1232 helix: -1.86 (0.20), residues: 380 sheet: -1.31 (0.35), residues: 212 loop : -1.40 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 199 TYR 0.007 0.001 TYR A 256 PHE 0.023 0.002 PHE A 71 TRP 0.009 0.001 TRP C 56 HIS 0.002 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.01151 / 0.50 (10248) covalent geometry : angle 1.05750 / 0.49 (13952) SS BOND : bond 0.00103 / 0.05 ( 4) SS BOND : angle 0.42922 / 0.25 ( 8) hydrogen bonds : bond 0.15030 / 10.12 ( 447) hydrogen bonds : angle 7.22112 / 5.03 ( 1341) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.555 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: symmetry clash REVERT: A 54 ASP cc_start: 0.7489 (t0) cc_final: 0.6769 (t0) REVERT: A 205 LYS cc_start: 0.8525 (mttt) cc_final: 0.8277 (mttm) REVERT: A 206 SER cc_start: 0.8541 (t) cc_final: 0.8246 (p) REVERT: B 54 ASP cc_start: 0.7573 (t0) cc_final: 0.6891 (t0) REVERT: B 158 GLU cc_start: 0.7750 (tt0) cc_final: 0.7490 (tm-30) REVERT: C 54 ASP cc_start: 0.7584 (t0) cc_final: 0.6909 (t0) REVERT: C 158 GLU cc_start: 0.7752 (tt0) cc_final: 0.7488 (tm-30) REVERT: D 54 ASP cc_start: 0.7567 (t0) cc_final: 0.6892 (t0) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 1.1886 time to fit residues: 313.7846 Evaluate side-chains 101 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 GLN A 228 ASN A 232 ASN B 183 GLN B 228 ASN B 232 ASN C 183 GLN C 228 ASN C 232 ASN D 183 GLN D 228 ASN D 232 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.115548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.084356 restraints weight = 57873.572| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 3.20 r_work: 0.3147 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10252 Z= 0.129 Angle : 0.537 3.845 13960 Z= 0.291 Chirality : 0.042 0.151 1652 Planarity : 0.005 0.049 1708 Dihedral : 6.355 43.189 1368 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.19 % Allowed : 8.73 % Favored : 90.07 % 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: 0.03 (0.23), residues: 1232 helix: 1.16 (0.25), residues: 380 sheet: -0.09 (0.37), residues: 208 loop : -0.60 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 40 TYR 0.005 0.001 TYR A 323 PHE 0.014 0.001 PHE C 165 TRP 0.008 0.001 TRP D 56 HIS 0.010 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (10248) covalent geometry : angle 0.53717 / 0.29 (13952) SS BOND : bond 0.00171 / 0.09 ( 4) SS BOND : angle 0.92937 / 0.60 ( 8) hydrogen bonds : bond 0.05571 / 3.73 ( 447) hydrogen bonds : angle 5.23031 / 3.72 ( 1341) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.483 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 205 LYS cc_start: 0.8738 (mttt) cc_final: 0.8504 (mttm) REVERT: B 158 GLU cc_start: 0.8520 (tt0) cc_final: 0.7929 (tm-30) REVERT: B 203 MET cc_start: 0.8968 (mmm) cc_final: 0.8657 (mmt) REVERT: B 256 TYR cc_start: 0.9059 (p90) cc_final: 0.8831 (p90) REVERT: C 203 MET cc_start: 0.8975 (mmm) cc_final: 0.8659 (mmt) REVERT: D 203 MET cc_start: 0.8947 (mmm) cc_final: 0.8682 (mmt) outliers start: 13 outliers final: 1 residues processed: 150 average time/residue: 0.8833 time to fit residues: 145.9848 Evaluate side-chains 127 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 65 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 94 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 121 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.113619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.082042 restraints weight = 58920.531| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.19 r_work: 0.3107 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10252 Z= 0.135 Angle : 0.489 3.900 13960 Z= 0.261 Chirality : 0.041 0.136 1652 Planarity : 0.003 0.040 1708 Dihedral : 5.544 44.717 1368 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.65 % Allowed : 10.11 % Favored : 88.24 % 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: 0.96 (0.24), residues: 1232 helix: 2.18 (0.25), residues: 384 sheet: 0.41 (0.37), residues: 208 loop : -0.20 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 40 TYR 0.003 0.001 TYR A 300 PHE 0.012 0.001 PHE D 165 TRP 0.006 0.001 TRP B 56 HIS 0.006 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (10248) covalent geometry : angle 0.48821 / 0.26 (13952) SS BOND : bond 0.00460 / 0.24 ( 4) SS BOND : angle 1.20155 / 0.76 ( 8) hydrogen bonds : bond 0.05083 / 3.40 ( 447) hydrogen bonds : angle 4.78142 / 3.40 ( 1341) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.503 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: A 205 LYS cc_start: 0.8705 (mttt) cc_final: 0.8499 (mttm) REVERT: A 327 PHE cc_start: 0.7676 (m-80) cc_final: 0.7416 (m-80) REVERT: B 158 GLU cc_start: 0.8673 (tt0) cc_final: 0.8121 (tm-30) REVERT: B 203 MET cc_start: 0.9080 (mmm) cc_final: 0.8792 (mmt) REVERT: B 256 TYR cc_start: 0.8985 (p90) cc_final: 0.8754 (p90) REVERT: B 276 ASP cc_start: 0.8271 (t0) cc_final: 0.8068 (t0) REVERT: B 327 PHE cc_start: 0.7603 (m-80) cc_final: 0.7384 (m-80) REVERT: C 158 GLU cc_start: 0.8652 (tt0) cc_final: 0.8144 (tm-30) REVERT: C 203 MET cc_start: 0.9093 (mmm) cc_final: 0.8757 (mmt) REVERT: C 256 TYR cc_start: 0.8946 (p90) cc_final: 0.8724 (p90) REVERT: D 158 GLU cc_start: 0.8638 (tt0) cc_final: 0.8077 (tm-30) REVERT: D 203 MET cc_start: 0.9123 (mmm) cc_final: 0.8857 (mmt) REVERT: D 256 TYR cc_start: 0.8903 (p90) cc_final: 0.8698 (p90) REVERT: D 327 PHE cc_start: 0.7508 (m-80) cc_final: 0.7127 (m-80) outliers start: 18 outliers final: 11 residues processed: 141 average time/residue: 1.1268 time to fit residues: 172.1782 Evaluate side-chains 128 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 315 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 121 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 GLN B 295 GLN C 221 HIS ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.110314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.078157 restraints weight = 58800.387| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 3.13 r_work: 0.3040 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10252 Z= 0.196 Angle : 0.504 3.924 13960 Z= 0.272 Chirality : 0.041 0.154 1652 Planarity : 0.003 0.034 1708 Dihedral : 5.551 52.091 1368 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.03 % Allowed : 11.12 % Favored : 85.85 % 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: 1.37 (0.24), residues: 1232 helix: 2.38 (0.25), residues: 384 sheet: 0.65 (0.37), residues: 212 loop : 0.14 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 40 TYR 0.006 0.001 TYR A 256 PHE 0.011 0.001 PHE A 71 TRP 0.007 0.001 TRP B 56 HIS 0.005 0.001 HIS B 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 (10248) covalent geometry : angle 0.50331 / 0.27 (13952) SS BOND : bond 0.00198 / 0.10 ( 4) SS BOND : angle 1.18983 / 0.77 ( 8) hydrogen bonds : bond 0.05281 / 3.51 ( 447) hydrogen bonds : angle 4.70446 / 3.35 ( 1341) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.543 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: A 136 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.9095 (tt) REVERT: A 205 LYS cc_start: 0.8746 (mttt) cc_final: 0.8483 (mppt) REVERT: B 158 GLU cc_start: 0.8745 (tt0) cc_final: 0.8245 (tm-30) REVERT: B 203 MET cc_start: 0.9051 (mmm) cc_final: 0.8694 (mmt) REVERT: C 54 ASP cc_start: 0.7369 (t0) cc_final: 0.7147 (t0) REVERT: C 158 GLU cc_start: 0.8736 (tt0) cc_final: 0.8227 (tm-30) REVERT: C 203 MET cc_start: 0.9061 (mmm) cc_final: 0.8743 (mmt) REVERT: C 221 HIS cc_start: 0.8348 (m-70) cc_final: 0.8079 (m-70) REVERT: C 256 TYR cc_start: 0.8945 (p90) cc_final: 0.8713 (p90) REVERT: D 54 ASP cc_start: 0.7410 (t0) cc_final: 0.7132 (t0) REVERT: D 158 GLU cc_start: 0.8712 (tt0) cc_final: 0.8207 (tm-30) REVERT: D 203 MET cc_start: 0.9118 (mmm) cc_final: 0.8811 (mmt) REVERT: D 221 HIS cc_start: 0.8373 (m-70) cc_final: 0.8100 (m-70) REVERT: D 256 TYR cc_start: 0.8944 (p90) cc_final: 0.8738 (p90) outliers start: 33 outliers final: 16 residues processed: 137 average time/residue: 0.9182 time to fit residues: 138.3485 Evaluate side-chains 119 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 315 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 9 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 221 HIS C 295 GLN D 221 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.108609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.076216 restraints weight = 58913.346| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.16 r_work: 0.3007 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10252 Z= 0.229 Angle : 0.523 3.923 13960 Z= 0.283 Chirality : 0.042 0.145 1652 Planarity : 0.003 0.039 1708 Dihedral : 5.633 52.705 1368 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.76 % Allowed : 11.95 % Favored : 85.29 % 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: 1.09 (0.24), residues: 1232 helix: 1.91 (0.25), residues: 404 sheet: 0.70 (0.37), residues: 212 loop : -0.00 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 36 TYR 0.006 0.001 TYR A 256 PHE 0.011 0.001 PHE A 71 TRP 0.007 0.001 TRP A 56 HIS 0.005 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.23 (10248) covalent geometry : angle 0.52191 / 0.28 (13952) SS BOND : bond 0.00214 / 0.11 ( 4) SS BOND : angle 1.23764 / 0.80 ( 8) hydrogen bonds : bond 0.05504 / 3.65 ( 447) hydrogen bonds : angle 4.69809 / 3.35 ( 1341) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.509 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: A 205 LYS cc_start: 0.8740 (mttt) cc_final: 0.8499 (mppt) REVERT: B 54 ASP cc_start: 0.7519 (t0) cc_final: 0.7232 (t0) REVERT: B 158 GLU cc_start: 0.8734 (tt0) cc_final: 0.8237 (tm-30) REVERT: B 203 MET cc_start: 0.9110 (mmm) cc_final: 0.8788 (mmt) REVERT: C 54 ASP cc_start: 0.7504 (t0) cc_final: 0.7155 (t0) REVERT: C 158 GLU cc_start: 0.8737 (tt0) cc_final: 0.8227 (tm-30) REVERT: C 203 MET cc_start: 0.9117 (mmm) cc_final: 0.8791 (mmt) REVERT: D 54 ASP cc_start: 0.7488 (t0) cc_final: 0.7128 (t0) REVERT: D 158 GLU cc_start: 0.8705 (tt0) cc_final: 0.8201 (tm-30) REVERT: D 203 MET cc_start: 0.9197 (mmm) cc_final: 0.8941 (mmt) REVERT: D 327 PHE cc_start: 0.7655 (m-80) cc_final: 0.7386 (m-80) REVERT: D 332 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8384 (mp10) outliers start: 30 outliers final: 18 residues processed: 117 average time/residue: 1.0296 time to fit residues: 132.0597 Evaluate side-chains 123 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 332 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 88 optimal weight: 0.0070 chunk 51 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 overall best weight: 3.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.109159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.077057 restraints weight = 58456.125| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 3.13 r_work: 0.3023 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10252 Z= 0.173 Angle : 0.480 3.815 13960 Z= 0.260 Chirality : 0.041 0.135 1652 Planarity : 0.003 0.041 1708 Dihedral : 5.504 53.221 1368 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.65 % Allowed : 13.60 % Favored : 84.74 % 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: 1.20 (0.25), residues: 1232 helix: 1.88 (0.26), residues: 408 sheet: 0.82 (0.37), residues: 212 loop : 0.13 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 36 TYR 0.007 0.001 TYR D 256 PHE 0.010 0.001 PHE B 71 TRP 0.007 0.001 TRP B 56 HIS 0.004 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (10248) covalent geometry : angle 0.47919 / 0.26 (13952) SS BOND : bond 0.00149 / 0.08 ( 4) SS BOND : angle 1.01087 / 0.67 ( 8) hydrogen bonds : bond 0.05191 / 3.44 ( 447) hydrogen bonds : angle 4.55896 / 3.24 ( 1341) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.684 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: A 205 LYS cc_start: 0.8726 (mttt) cc_final: 0.8498 (mppt) REVERT: B 54 ASP cc_start: 0.7431 (t0) cc_final: 0.7215 (t0) REVERT: B 158 GLU cc_start: 0.8717 (tt0) cc_final: 0.8219 (tm-30) REVERT: C 54 ASP cc_start: 0.7486 (t0) cc_final: 0.7206 (t0) REVERT: C 158 GLU cc_start: 0.8724 (tt0) cc_final: 0.8214 (tm-30) REVERT: C 228 ASN cc_start: 0.8496 (m-40) cc_final: 0.8106 (p0) REVERT: C 256 TYR cc_start: 0.8920 (p90) cc_final: 0.8658 (p90) REVERT: D 54 ASP cc_start: 0.7474 (t0) cc_final: 0.7184 (t0) REVERT: D 158 GLU cc_start: 0.8684 (tt0) cc_final: 0.8190 (tm-30) REVERT: D 203 MET cc_start: 0.9224 (mmm) cc_final: 0.8961 (mmt) REVERT: D 228 ASN cc_start: 0.8488 (m-40) cc_final: 0.8082 (p0) REVERT: D 256 TYR cc_start: 0.8881 (p90) cc_final: 0.8629 (p90) outliers start: 18 outliers final: 12 residues processed: 113 average time/residue: 1.0440 time to fit residues: 129.1954 Evaluate side-chains 118 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 276 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 315 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 115 optimal weight: 0.6980 chunk 52 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 98 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.109338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.077396 restraints weight = 58546.748| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.13 r_work: 0.3023 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10252 Z= 0.162 Angle : 0.478 4.226 13960 Z= 0.258 Chirality : 0.040 0.139 1652 Planarity : 0.003 0.033 1708 Dihedral : 5.442 53.529 1368 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.21 % Allowed : 13.33 % Favored : 84.47 % 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: 1.28 (0.25), residues: 1232 helix: 1.90 (0.26), residues: 408 sheet: 0.82 (0.36), residues: 212 loop : 0.22 (0.27), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 36 TYR 0.005 0.001 TYR B 256 PHE 0.010 0.001 PHE A 71 TRP 0.006 0.001 TRP B 56 HIS 0.005 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (10248) covalent geometry : angle 0.47760 / 0.26 (13952) SS BOND : bond 0.00127 / 0.07 ( 4) SS BOND : angle 0.94484 / 0.62 ( 8) hydrogen bonds : bond 0.05125 / 3.39 ( 447) hydrogen bonds : angle 4.51691 / 3.22 ( 1341) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.556 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: A 205 LYS cc_start: 0.8744 (mttt) cc_final: 0.8523 (mppt) REVERT: B 158 GLU cc_start: 0.8725 (tt0) cc_final: 0.8226 (tm-30) REVERT: C 54 ASP cc_start: 0.7471 (t0) cc_final: 0.7184 (t0) REVERT: C 158 GLU cc_start: 0.8726 (tt0) cc_final: 0.8216 (tm-30) REVERT: C 256 TYR cc_start: 0.8895 (p90) cc_final: 0.8671 (p90) REVERT: D 54 ASP cc_start: 0.7464 (t0) cc_final: 0.7171 (t0) REVERT: D 158 GLU cc_start: 0.8701 (tt0) cc_final: 0.8204 (tm-30) REVERT: D 228 ASN cc_start: 0.8483 (m-40) cc_final: 0.8161 (p0) REVERT: D 256 TYR cc_start: 0.8911 (p90) cc_final: 0.8645 (p90) outliers start: 24 outliers final: 17 residues processed: 119 average time/residue: 0.9695 time to fit residues: 127.0041 Evaluate side-chains 115 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 317 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 4 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 70 optimal weight: 0.0970 chunk 50 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.110529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.078846 restraints weight = 58321.559| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 3.08 r_work: 0.3045 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10252 Z= 0.126 Angle : 0.464 4.277 13960 Z= 0.248 Chirality : 0.040 0.138 1652 Planarity : 0.003 0.030 1708 Dihedral : 5.331 54.274 1368 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.11 % Allowed : 13.79 % Favored : 84.10 % 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: 1.34 (0.25), residues: 1232 helix: 2.00 (0.26), residues: 408 sheet: 0.78 (0.35), residues: 212 loop : 0.24 (0.27), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 36 TYR 0.006 0.001 TYR D 256 PHE 0.010 0.001 PHE A 71 TRP 0.006 0.001 TRP B 56 HIS 0.004 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (10248) covalent geometry : angle 0.46365 / 0.25 (13952) SS BOND : bond 0.00102 / 0.05 ( 4) SS BOND : angle 0.86866 / 0.58 ( 8) hydrogen bonds : bond 0.04870 / 3.22 ( 447) hydrogen bonds : angle 4.40219 / 3.14 ( 1341) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.501 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: A 205 LYS cc_start: 0.8716 (mttt) cc_final: 0.8497 (mppt) REVERT: A 221 HIS cc_start: 0.8612 (OUTLIER) cc_final: 0.8303 (m-70) REVERT: A 327 PHE cc_start: 0.7848 (m-80) cc_final: 0.7434 (m-80) REVERT: B 41 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8083 (mmt) REVERT: B 158 GLU cc_start: 0.8717 (tt0) cc_final: 0.8212 (tm-30) REVERT: B 221 HIS cc_start: 0.8652 (OUTLIER) cc_final: 0.8378 (m-70) REVERT: C 54 ASP cc_start: 0.7406 (t0) cc_final: 0.7152 (t0) REVERT: C 158 GLU cc_start: 0.8716 (tt0) cc_final: 0.8217 (tm-30) REVERT: C 228 ASN cc_start: 0.8516 (m-40) cc_final: 0.8243 (p0) REVERT: C 256 TYR cc_start: 0.8901 (p90) cc_final: 0.8662 (p90) REVERT: D 54 ASP cc_start: 0.7400 (t0) cc_final: 0.7140 (t0) REVERT: D 158 GLU cc_start: 0.8697 (tt0) cc_final: 0.8193 (tm-30) REVERT: D 228 ASN cc_start: 0.8509 (m-40) cc_final: 0.8244 (p0) REVERT: D 256 TYR cc_start: 0.8906 (p90) cc_final: 0.8685 (p90) outliers start: 23 outliers final: 16 residues processed: 115 average time/residue: 1.0605 time to fit residues: 132.9161 Evaluate side-chains 121 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 221 HIS Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 317 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 51 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.108822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.076608 restraints weight = 59284.921| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.20 r_work: 0.3001 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 10252 Z= 0.210 Angle : 0.512 4.779 13960 Z= 0.275 Chirality : 0.041 0.131 1652 Planarity : 0.003 0.030 1708 Dihedral : 5.412 53.411 1368 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.02 % Allowed : 13.79 % Favored : 84.19 % 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: 1.26 (0.25), residues: 1232 helix: 1.87 (0.26), residues: 408 sheet: 0.79 (0.35), residues: 212 loop : 0.23 (0.27), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 204 TYR 0.006 0.001 TYR B 66 PHE 0.011 0.001 PHE B 71 TRP 0.006 0.001 TRP A 56 HIS 0.004 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.21 (10248) covalent geometry : angle 0.51150 / 0.28 (13952) SS BOND : bond 0.00157 / 0.08 ( 4) SS BOND : angle 1.12055 / 0.77 ( 8) hydrogen bonds : bond 0.05307 / 3.52 ( 447) hydrogen bonds : angle 4.53477 / 3.23 ( 1341) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.509 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: A 205 LYS cc_start: 0.8747 (mttt) cc_final: 0.8528 (mppt) REVERT: A 221 HIS cc_start: 0.8634 (OUTLIER) cc_final: 0.8355 (m-70) REVERT: B 158 GLU cc_start: 0.8731 (tt0) cc_final: 0.8231 (tm-30) REVERT: B 221 HIS cc_start: 0.8671 (OUTLIER) cc_final: 0.8394 (m-70) REVERT: B 276 ASP cc_start: 0.8353 (t0) cc_final: 0.7951 (t0) REVERT: C 54 ASP cc_start: 0.7507 (t0) cc_final: 0.7188 (t0) REVERT: C 158 GLU cc_start: 0.8735 (tt0) cc_final: 0.8223 (tm-30) REVERT: C 256 TYR cc_start: 0.8887 (p90) cc_final: 0.8636 (p90) REVERT: D 54 ASP cc_start: 0.7494 (t0) cc_final: 0.7164 (t0) REVERT: D 158 GLU cc_start: 0.8725 (tt0) cc_final: 0.8219 (tm-30) REVERT: D 197 MET cc_start: 0.9392 (mmm) cc_final: 0.9185 (mmt) REVERT: D 228 ASN cc_start: 0.8478 (m-40) cc_final: 0.8244 (p0) REVERT: D 256 TYR cc_start: 0.8921 (p90) cc_final: 0.8697 (p90) outliers start: 22 outliers final: 16 residues processed: 116 average time/residue: 1.0144 time to fit residues: 129.0386 Evaluate side-chains 111 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 221 HIS Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 317 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 103 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 87 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 113 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.110856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.078963 restraints weight = 58871.216| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.19 r_work: 0.3041 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10252 Z= 0.121 Angle : 0.467 5.032 13960 Z= 0.249 Chirality : 0.040 0.132 1652 Planarity : 0.003 0.029 1708 Dihedral : 5.282 53.982 1368 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.65 % Allowed : 14.43 % Favored : 83.92 % 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: 1.38 (0.25), residues: 1232 helix: 2.00 (0.26), residues: 408 sheet: 0.87 (0.35), residues: 212 loop : 0.27 (0.27), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 230 TYR 0.006 0.001 TYR D 256 PHE 0.010 0.001 PHE B 71 TRP 0.007 0.001 TRP A 56 HIS 0.005 0.001 HIS C 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (10248) covalent geometry : angle 0.46695 / 0.25 (13952) SS BOND : bond 0.00098 / 0.05 ( 4) SS BOND : angle 0.84912 / 0.59 ( 8) hydrogen bonds : bond 0.04845 / 3.20 ( 447) hydrogen bonds : angle 4.35415 / 3.11 ( 1341) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.580 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: A 205 LYS cc_start: 0.8748 (mttt) cc_final: 0.8524 (mppt) REVERT: A 221 HIS cc_start: 0.8625 (OUTLIER) cc_final: 0.8358 (m-70) REVERT: B 158 GLU cc_start: 0.8729 (tt0) cc_final: 0.8237 (tm-30) REVERT: B 197 MET cc_start: 0.9267 (mmm) cc_final: 0.9039 (mmt) REVERT: C 158 GLU cc_start: 0.8719 (tt0) cc_final: 0.8223 (tm-30) REVERT: C 256 TYR cc_start: 0.8893 (p90) cc_final: 0.8629 (p90) REVERT: D 158 GLU cc_start: 0.8711 (tt0) cc_final: 0.8220 (tm-30) REVERT: D 197 MET cc_start: 0.9339 (mmm) cc_final: 0.9138 (mmt) REVERT: D 228 ASN cc_start: 0.8530 (m-40) cc_final: 0.8297 (p0) REVERT: D 256 TYR cc_start: 0.8919 (p90) cc_final: 0.8688 (p90) outliers start: 18 outliers final: 16 residues processed: 106 average time/residue: 1.0556 time to fit residues: 122.1754 Evaluate side-chains 107 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 317 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 32 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.109898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.077832 restraints weight = 58309.308| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.13 r_work: 0.3029 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10252 Z= 0.155 Angle : 0.480 4.868 13960 Z= 0.257 Chirality : 0.040 0.140 1652 Planarity : 0.003 0.028 1708 Dihedral : 5.285 54.347 1368 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.84 % Allowed : 14.34 % Favored : 83.82 % 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: 1.36 (0.25), residues: 1232 helix: 1.97 (0.26), residues: 408 sheet: 0.90 (0.35), residues: 212 loop : 0.27 (0.27), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 230 TYR 0.005 0.001 TYR A 256 PHE 0.011 0.001 PHE A 71 TRP 0.006 0.001 TRP A 56 HIS 0.004 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (10248) covalent geometry : angle 0.47925 / 0.26 (13952) SS BOND : bond 0.00122 / 0.06 ( 4) SS BOND : angle 0.97151 / 0.68 ( 8) hydrogen bonds : bond 0.04990 / 3.30 ( 447) hydrogen bonds : angle 4.39010 / 3.13 ( 1341) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5522.40 seconds wall clock time: 94 minutes 17.22 seconds (5657.22 seconds total)