Starting phenix.real_space_refine on Wed Mar 4 23:51:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p8w_13256/03_2026/7p8w_13256.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p8w_13256/03_2026/7p8w_13256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p8w_13256/03_2026/7p8w_13256.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p8w_13256/03_2026/7p8w_13256.map" model { file = "/net/cci-nas-00/data/ceres_data/7p8w_13256/03_2026/7p8w_13256.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p8w_13256/03_2026/7p8w_13256.cif" } resolution = 2.2 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= 0.004 sd= 0.031 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 Fe 4 7.16 5 P 12 5.49 5 S 52 5.16 5 C 10504 2.51 5 N 2920 2.21 5 O 4176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17668 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4047 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 502, 4037 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 464} Conformer: "B" Number of residues, atoms: 502, 4037 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 464} bond proxies already assigned to first conformer: 4145 Chain: "B" Number of atoms: 4047 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 502, 4037 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 464} Conformer: "B" Number of residues, atoms: 502, 4037 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 464} bond proxies already assigned to first conformer: 4145 Chain: "C" Number of atoms: 4047 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 502, 4037 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 464} Conformer: "B" Number of residues, atoms: 502, 4037 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 464} bond proxies already assigned to first conformer: 4145 Chain: "D" Number of atoms: 4047 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 502, 4037 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 464} Conformer: "B" Number of residues, atoms: 502, 4037 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 464} bond proxies already assigned to first conformer: 4145 Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 281 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 279, 279 Classifications: {'water': 279} Link IDs: {None: 278} Conformer: "B" Number of residues, atoms: 279, 279 Classifications: {'water': 279} Link IDs: {None: 278} Chain: "B" Number of atoms: 280 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 278, 278 Classifications: {'water': 278} Link IDs: {None: 277} Conformer: "B" Number of residues, atoms: 278, 278 Classifications: {'water': 278} Link IDs: {None: 277} Chain: "C" Number of atoms: 277 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 276, 276 Classifications: {'water': 276} Link IDs: {None: 275} Conformer: "B" Number of residues, atoms: 276, 276 Classifications: {'water': 276} Link IDs: {None: 275} Chain: "D" Number of atoms: 278 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 277, 277 Classifications: {'water': 277} Link IDs: {None: 276} Conformer: "B" Number of residues, atoms: 277, 277 Classifications: {'water': 277} Link IDs: {None: 276} Residues with excluded nonbonded symmetry interactions: 10 residue: pdb=" N AHIS A 372 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 372 " occ=0.50 residue: pdb=" N AHIS B 372 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 372 " occ=0.50 residue: pdb=" N AHIS C 372 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS C 372 " occ=0.50 residue: pdb=" N AHIS D 372 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS D 372 " occ=0.50 residue: pdb=" O AHOH A 858 " occ=0.50 pdb=" O BHOH A 858 " occ=0.50 residue: pdb=" O AHOH A 965 " occ=0.50 pdb=" O BHOH A 965 " occ=0.50 residue: pdb=" O AHOH B 857 " occ=0.50 pdb=" O BHOH B 857 " occ=0.50 residue: pdb=" O AHOH B 964 " occ=0.50 pdb=" O BHOH B 964 " occ=0.50 residue: pdb=" O AHOH C 853 " occ=0.50 pdb=" O BHOH C 853 " occ=0.50 residue: pdb=" O AHOH D 847 " occ=0.50 pdb=" O BHOH D 847 " occ=0.50 Time building chain proxies: 7.29, per 1000 atoms: 0.41 Number of scatterers: 17668 At special positions: 0 Unit cell: (108.102, 110.242, 84.5547, 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) Fe 4 26.01 S 52 16.00 P 12 15.00 O 4176 8.00 N 2920 7.00 C 10504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 1.1 seconds 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3760 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 8 sheets defined 41.2% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 54 through 65 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 178 through 189 Processing helix chain 'A' and resid 192 through 201 Processing helix chain 'A' and resid 202 through 205 Processing helix chain 'A' and resid 208 through 212 removed outlier: 3.837A pdb=" N HIS A 211 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET A 212 " --> pdb=" O HIS A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 212' Processing helix chain 'A' and resid 246 through 257 removed outlier: 3.503A pdb=" N GLN A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 271 Processing helix chain 'A' and resid 285 through 292 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 348 through 366 removed outlier: 3.736A pdb=" N PHE A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A 358 " --> pdb=" O ARG A 354 " (cutoff:3.500A) Proline residue: A 359 - end of helix removed outlier: 3.558A pdb=" N HIS A 364 " --> pdb=" O ASP A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 377 Proline residue: A 374 - end of helix Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 440 through 450 Processing helix chain 'A' and resid 452 through 468 Processing helix chain 'A' and resid 471 through 486 removed outlier: 3.507A pdb=" N VAL A 485 " --> pdb=" O ASN A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 504 Processing helix chain 'B' and resid 10 through 20 Processing helix chain 'B' and resid 54 through 65 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 160 through 169 Processing helix chain 'B' and resid 178 through 189 Processing helix chain 'B' and resid 192 through 201 Processing helix chain 'B' and resid 202 through 205 Processing helix chain 'B' and resid 208 through 212 removed outlier: 3.837A pdb=" N HIS B 211 " --> pdb=" O GLY B 208 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET B 212 " --> pdb=" O HIS B 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 208 through 212' Processing helix chain 'B' and resid 246 through 257 removed outlier: 3.504A pdb=" N GLN B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 285 through 292 Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 348 through 366 removed outlier: 3.736A pdb=" N PHE B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR B 358 " --> pdb=" O ARG B 354 " (cutoff:3.500A) Proline residue: B 359 - end of helix removed outlier: 3.558A pdb=" N HIS B 364 " --> pdb=" O ASP B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 377 Proline residue: B 374 - end of helix Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 440 through 450 Processing helix chain 'B' and resid 452 through 468 Processing helix chain 'B' and resid 471 through 486 removed outlier: 3.507A pdb=" N VAL B 485 " --> pdb=" O ASN B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 504 Processing helix chain 'C' and resid 10 through 20 Processing helix chain 'C' and resid 54 through 65 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'C' and resid 160 through 169 Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'C' and resid 192 through 201 Processing helix chain 'C' and resid 202 through 205 Processing helix chain 'C' and resid 208 through 212 removed outlier: 3.837A pdb=" N HIS C 211 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET C 212 " --> pdb=" O HIS C 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 208 through 212' Processing helix chain 'C' and resid 246 through 257 removed outlier: 3.504A pdb=" N GLN C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 271 Processing helix chain 'C' and resid 285 through 292 Processing helix chain 'C' and resid 324 through 329 Processing helix chain 'C' and resid 348 through 366 removed outlier: 3.736A pdb=" N PHE C 356 " --> pdb=" O GLN C 352 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR C 358 " --> pdb=" O ARG C 354 " (cutoff:3.500A) Proline residue: C 359 - end of helix removed outlier: 3.558A pdb=" N HIS C 364 " --> pdb=" O ASP C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 377 Proline residue: C 374 - end of helix Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 440 through 450 Processing helix chain 'C' and resid 452 through 468 Processing helix chain 'C' and resid 471 through 486 removed outlier: 3.507A pdb=" N VAL C 485 " --> pdb=" O ASN C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 504 Processing helix chain 'D' and resid 10 through 20 Processing helix chain 'D' and resid 54 through 65 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 157 through 159 No H-bonds generated for 'chain 'D' and resid 157 through 159' Processing helix chain 'D' and resid 160 through 169 Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 192 through 201 Processing helix chain 'D' and resid 202 through 205 Processing helix chain 'D' and resid 208 through 212 removed outlier: 3.837A pdb=" N HIS D 211 " --> pdb=" O GLY D 208 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET D 212 " --> pdb=" O HIS D 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 208 through 212' Processing helix chain 'D' and resid 246 through 257 removed outlier: 3.504A pdb=" N GLN D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 271 Processing helix chain 'D' and resid 285 through 292 Processing helix chain 'D' and resid 324 through 329 Processing helix chain 'D' and resid 348 through 366 removed outlier: 3.736A pdb=" N PHE D 356 " --> pdb=" O GLN D 352 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR D 358 " --> pdb=" O ARG D 354 " (cutoff:3.500A) Proline residue: D 359 - end of helix removed outlier: 3.557A pdb=" N HIS D 364 " --> pdb=" O ASP D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 377 Proline residue: D 374 - end of helix Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'D' and resid 440 through 450 Processing helix chain 'D' and resid 452 through 468 Processing helix chain 'D' and resid 471 through 486 removed outlier: 3.508A pdb=" N VAL D 485 " --> pdb=" O ASN D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 504 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 44 removed outlier: 3.899A pdb=" N ILE B 423 " --> pdb=" O VAL D 429 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 343 through 345 removed outlier: 6.453A pdb=" N TRP A 277 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS A 315 " --> pdb=" O TRP A 277 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE A 279 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU A 316 " --> pdb=" O GLU A 86 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLU A 86 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU A 318 " --> pdb=" O TYR A 84 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N TYR A 84 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 423 through 424 removed outlier: 3.899A pdb=" N ILE A 423 " --> pdb=" O VAL C 429 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 423 through 424 removed outlier: 3.899A pdb=" N ILE C 423 " --> pdb=" O VAL A 429 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 343 through 345 removed outlier: 6.454A pdb=" N TRP B 277 " --> pdb=" O LYS B 315 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS B 315 " --> pdb=" O TRP B 277 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE B 279 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU B 316 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLU B 86 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU B 318 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N TYR B 84 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 42 through 44 removed outlier: 3.899A pdb=" N ILE D 423 " --> pdb=" O VAL B 429 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 343 through 345 removed outlier: 6.453A pdb=" N TRP C 277 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS C 315 " --> pdb=" O TRP C 277 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N PHE C 279 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU C 316 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLU C 86 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU C 318 " --> pdb=" O TYR C 84 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N TYR C 84 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 343 through 345 removed outlier: 6.453A pdb=" N TRP D 277 " --> pdb=" O LYS D 315 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS D 315 " --> pdb=" O TRP D 277 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N PHE D 279 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU D 316 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLU D 86 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU D 318 " --> pdb=" O TYR D 84 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N TYR D 84 " --> pdb=" O LEU D 318 " (cutoff:3.500A) 680 hydrogen bonds defined for protein. 1872 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: 3.00 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.37: 5922 1.37 - 1.55: 11038 1.55 - 1.73: 20 1.73 - 1.91: 92 1.91 - 2.09: 12 Bond restraints: 17084 Sorted by residual: bond pdb=" O2B NDP B 601 " pdb=" P2B NDP B 601 " ideal model delta sigma weight residual 1.833 1.615 0.218 3.80e-02 6.93e+02 3.29e+01 bond pdb=" O2B NDP D 601 " pdb=" P2B NDP D 601 " ideal model delta sigma weight residual 1.833 1.615 0.218 3.80e-02 6.93e+02 3.28e+01 bond pdb=" O2B NDP A 601 " pdb=" P2B NDP A 601 " ideal model delta sigma weight residual 1.833 1.616 0.217 3.80e-02 6.93e+02 3.28e+01 bond pdb=" O2B NDP C 601 " pdb=" P2B NDP C 601 " ideal model delta sigma weight residual 1.833 1.616 0.217 3.80e-02 6.93e+02 3.27e+01 bond pdb=" O5D NDP A 601 " pdb=" PN NDP A 601 " ideal model delta sigma weight residual 1.757 1.589 0.168 3.50e-02 8.16e+02 2.29e+01 ... (remaining 17079 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.27: 23148 5.27 - 10.53: 148 10.53 - 15.80: 4 15.80 - 21.07: 8 21.07 - 26.33: 4 Bond angle restraints: 23312 Sorted by residual: angle pdb=" PA NDP A 601 " pdb=" O3 NDP A 601 " pdb=" PN NDP A 601 " ideal model delta sigma weight residual 107.74 134.07 -26.33 1.95e+00 2.62e-01 1.82e+02 angle pdb=" PA NDP D 601 " pdb=" O3 NDP D 601 " pdb=" PN NDP D 601 " ideal model delta sigma weight residual 107.74 134.07 -26.33 1.95e+00 2.62e-01 1.82e+02 angle pdb=" PA NDP B 601 " pdb=" O3 NDP B 601 " pdb=" PN NDP B 601 " ideal model delta sigma weight residual 107.74 134.06 -26.32 1.95e+00 2.62e-01 1.81e+02 angle pdb=" PA NDP C 601 " pdb=" O3 NDP C 601 " pdb=" PN NDP C 601 " ideal model delta sigma weight residual 107.74 134.06 -26.32 1.95e+00 2.62e-01 1.81e+02 angle pdb=" C5B NDP C 601 " pdb=" O5B NDP C 601 " pdb=" PA NDP C 601 " ideal model delta sigma weight residual 103.84 119.78 -15.94 1.91e+00 2.73e-01 6.93e+01 ... (remaining 23307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.02: 9341 21.02 - 42.04: 491 42.04 - 63.06: 100 63.06 - 84.09: 44 84.09 - 105.11: 12 Dihedral angle restraints: 9988 sinusoidal: 4132 harmonic: 5856 Sorted by residual: dihedral pdb=" CA ILE B 281 " pdb=" C ILE B 281 " pdb=" N GLN B 282 " pdb=" CA GLN B 282 " ideal model delta harmonic sigma weight residual 180.00 155.68 24.32 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA ILE A 281 " pdb=" C ILE A 281 " pdb=" N GLN A 282 " pdb=" CA GLN A 282 " ideal model delta harmonic sigma weight residual 180.00 155.70 24.30 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA ILE C 281 " pdb=" C ILE C 281 " pdb=" N GLN C 282 " pdb=" CA GLN C 282 " ideal model delta harmonic sigma weight residual 180.00 155.72 24.28 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 9985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1162 0.064 - 0.128: 819 0.128 - 0.192: 326 0.192 - 0.256: 37 0.256 - 0.320: 8 Chirality restraints: 2352 Sorted by residual: chirality pdb=" CA TYR B 236 " pdb=" N TYR B 236 " pdb=" C TYR B 236 " pdb=" CB TYR B 236 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA TYR C 236 " pdb=" N TYR C 236 " pdb=" C TYR C 236 " pdb=" CB TYR C 236 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA TYR D 236 " pdb=" N TYR D 236 " pdb=" C TYR D 236 " pdb=" CB TYR D 236 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 2349 not shown) Planarity restraints: 3092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP C 601 " -0.075 2.00e-02 2.50e+03 5.13e-02 3.29e+01 pdb=" C3N NDP C 601 " -0.031 2.00e-02 2.50e+03 pdb=" C4N NDP C 601 " -0.007 2.00e-02 2.50e+03 pdb=" C7N NDP C 601 " 0.050 2.00e-02 2.50e+03 pdb=" N1N NDP C 601 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP B 601 " 0.074 2.00e-02 2.50e+03 5.10e-02 3.26e+01 pdb=" C3N NDP B 601 " 0.031 2.00e-02 2.50e+03 pdb=" C4N NDP B 601 " 0.007 2.00e-02 2.50e+03 pdb=" C7N NDP B 601 " -0.049 2.00e-02 2.50e+03 pdb=" N1N NDP B 601 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP D 601 " -0.075 2.00e-02 2.50e+03 5.10e-02 3.26e+01 pdb=" C3N NDP D 601 " -0.031 2.00e-02 2.50e+03 pdb=" C4N NDP D 601 " -0.007 2.00e-02 2.50e+03 pdb=" C7N NDP D 601 " 0.049 2.00e-02 2.50e+03 pdb=" N1N NDP D 601 " 0.063 2.00e-02 2.50e+03 ... (remaining 3089 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 5749 2.85 - 3.36: 18510 3.36 - 3.88: 37900 3.88 - 4.39: 44424 4.39 - 4.90: 67343 Nonbonded interactions: 173926 Sorted by model distance: nonbonded pdb=" ND1 HIS C 364 " pdb=" O HOH C 701 " model vdw 2.340 3.120 nonbonded pdb=" ND1 HIS B 364 " pdb=" O HOH B 701 " model vdw 2.341 3.120 nonbonded pdb=" ND1 HIS D 364 " pdb=" O HOH D 701 " model vdw 2.342 3.120 nonbonded pdb=" ND1 HIS A 364 " pdb=" O HOH A 701 " model vdw 2.342 3.120 nonbonded pdb=" OE1 GLU A 191 " pdb=" O HOH A 702 " model vdw 2.413 3.040 ... (remaining 173921 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: 0.02 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=0.50 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: 0.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.860 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 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 : 0.014 0.218 17088 Z= 0.929 Angle : 1.791 26.335 23312 Z= 1.239 Chirality : 0.089 0.320 2352 Planarity : 0.008 0.051 3092 Dihedral : 14.824 105.107 6228 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.80 % Favored : 96.00 % Rotamer: Outliers : 0.75 % Allowed : 3.87 % Favored : 95.38 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 2.70 % 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 (0.16), residues: 2012 helix: -1.24 (0.15), residues: 692 sheet: 0.15 (0.28), residues: 284 loop : -0.86 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.003 ARG D 365 TYR 0.042 0.008 TYR B 236 PHE 0.051 0.008 PHE D 82 TRP 0.031 0.009 TRP D 15 HIS 0.014 0.005 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.01414 (17084) covalent geometry : angle 1.79106 (23312) hydrogen bonds : bond 0.18961 ( 680) hydrogen bonds : angle 8.43584 ( 1872) Misc. bond : bond 0.05397 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.703 Fit side-chains REVERT: A 18 GLN cc_start: 0.8170 (mt0) cc_final: 0.7910 (mp10) REVERT: A 23 LYS cc_start: 0.8087 (tttt) cc_final: 0.7793 (ptmm) REVERT: A 248 GLU cc_start: 0.8528 (tt0) cc_final: 0.8162 (mp0) REVERT: A 273 LYS cc_start: 0.8810 (mttp) cc_final: 0.8463 (mtpt) REVERT: A 306 LYS cc_start: 0.8915 (mtpt) cc_final: 0.8454 (mppt) REVERT: A 339 MET cc_start: 0.9072 (mtm) cc_final: 0.8517 (mtm) REVERT: A 382 ARG cc_start: 0.8732 (ttm110) cc_final: 0.8444 (ttm-80) REVERT: B 18 GLN cc_start: 0.8167 (mt0) cc_final: 0.7909 (mp10) REVERT: B 23 LYS cc_start: 0.8088 (tttt) cc_final: 0.7793 (ptmm) REVERT: B 248 GLU cc_start: 0.8525 (tt0) cc_final: 0.8162 (mp0) REVERT: B 273 LYS cc_start: 0.8811 (mttp) cc_final: 0.8465 (mtpt) REVERT: B 306 LYS cc_start: 0.8914 (mtpt) cc_final: 0.8453 (mppt) REVERT: B 339 MET cc_start: 0.9078 (mtm) cc_final: 0.8532 (mtm) REVERT: B 382 ARG cc_start: 0.8705 (ttm110) cc_final: 0.8431 (ttm-80) REVERT: C 18 GLN cc_start: 0.8169 (mt0) cc_final: 0.7910 (mp10) REVERT: C 23 LYS cc_start: 0.8087 (tttt) cc_final: 0.7790 (ptmm) REVERT: C 248 GLU cc_start: 0.8527 (tt0) cc_final: 0.8163 (mp0) REVERT: C 273 LYS cc_start: 0.8813 (mttp) cc_final: 0.8467 (mtpt) REVERT: C 306 LYS cc_start: 0.8916 (mtpt) cc_final: 0.8456 (mppt) REVERT: C 339 MET cc_start: 0.9072 (mtm) cc_final: 0.8517 (mtm) REVERT: C 382 ARG cc_start: 0.8703 (ttm110) cc_final: 0.8430 (ttm-80) REVERT: D 18 GLN cc_start: 0.8169 (mt0) cc_final: 0.7910 (mp10) REVERT: D 23 LYS cc_start: 0.8087 (tttt) cc_final: 0.7791 (ptmm) REVERT: D 248 GLU cc_start: 0.8524 (tt0) cc_final: 0.8160 (mp0) REVERT: D 273 LYS cc_start: 0.8809 (mttp) cc_final: 0.8463 (mtpt) REVERT: D 306 LYS cc_start: 0.8915 (mtpt) cc_final: 0.8454 (mppt) REVERT: D 339 MET cc_start: 0.9078 (mtm) cc_final: 0.8533 (mtm) REVERT: D 382 ARG cc_start: 0.8704 (ttm110) cc_final: 0.8431 (ttm-80) outliers start: 13 outliers final: 4 residues processed: 157 average time/residue: 0.8183 time to fit residues: 140.1993 Evaluate side-chains 116 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain D residue 138 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN A 449 ASN A 492 HIS B 168 GLN B 449 ASN B 492 HIS C 168 GLN C 449 ASN C 492 HIS D 168 GLN D 449 ASN D 492 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.093917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.072766 restraints weight = 41665.528| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 1.67 r_work: 0.2605 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2488 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2490 r_free = 0.2490 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2489 r_free = 0.2489 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2489 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9029 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 17088 Z= 0.187 Angle : 0.682 7.472 23312 Z= 0.353 Chirality : 0.049 0.167 2352 Planarity : 0.005 0.034 3092 Dihedral : 9.432 100.557 2284 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.73 % Allowed : 5.08 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.18), residues: 2012 helix: 0.89 (0.19), residues: 700 sheet: 0.46 (0.29), residues: 304 loop : -0.18 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 156 TYR 0.030 0.002 TYR A 236 PHE 0.024 0.003 PHE C 164 TRP 0.016 0.002 TRP B 183 HIS 0.006 0.002 HIS D 209 Details of bonding type rmsd covalent geometry : bond 0.00437 (17084) covalent geometry : angle 0.68166 (23312) hydrogen bonds : bond 0.05830 ( 680) hydrogen bonds : angle 6.33293 ( 1872) Misc. bond : bond 0.08466 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.467 Fit side-chains REVERT: A 256 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7949 (mt-10) REVERT: A 273 LYS cc_start: 0.8910 (mttp) cc_final: 0.8631 (mtpt) REVERT: A 306 LYS cc_start: 0.8705 (mtpt) cc_final: 0.8467 (mppt) REVERT: A 499 LYS cc_start: 0.8493 (tttm) cc_final: 0.8288 (mtpp) REVERT: B 256 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7954 (mt-10) REVERT: B 273 LYS cc_start: 0.8908 (mttp) cc_final: 0.8627 (mtpt) REVERT: B 306 LYS cc_start: 0.8714 (mtpt) cc_final: 0.8478 (mppt) REVERT: B 499 LYS cc_start: 0.8486 (tttm) cc_final: 0.8281 (mtpp) REVERT: C 256 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7953 (mt-10) REVERT: C 273 LYS cc_start: 0.8906 (mttp) cc_final: 0.8625 (mtpt) REVERT: C 306 LYS cc_start: 0.8702 (mtpt) cc_final: 0.8472 (mppt) REVERT: C 394 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.7506 (mpt) REVERT: C 499 LYS cc_start: 0.8461 (tttm) cc_final: 0.8257 (mtpp) REVERT: D 256 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7958 (mt-10) REVERT: D 273 LYS cc_start: 0.8902 (mttp) cc_final: 0.8619 (mtpt) REVERT: D 306 LYS cc_start: 0.8703 (mtpt) cc_final: 0.8473 (mppt) REVERT: D 394 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.7514 (mpt) REVERT: D 499 LYS cc_start: 0.8476 (tttm) cc_final: 0.8270 (mtpp) outliers start: 30 outliers final: 8 residues processed: 136 average time/residue: 0.7562 time to fit residues: 113.0854 Evaluate side-chains 134 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 394 MET Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 394 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 104 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 28 optimal weight: 0.7980 chunk 144 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 211 HIS A 372 HIS B B 18 GLN B 211 HIS B 372 HIS B C 18 GLN C 211 HIS C 372 HIS B D 18 GLN D 211 HIS D 372 HIS B Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.096176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.075975 restraints weight = 32396.168| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 1.49 r_work: 0.2677 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2560 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2560 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17088 Z= 0.145 Angle : 0.607 5.664 23312 Z= 0.311 Chirality : 0.046 0.164 2352 Planarity : 0.004 0.036 3092 Dihedral : 8.830 96.865 2284 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.15 % Allowed : 6.18 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.78 (0.18), residues: 2012 helix: 1.30 (0.20), residues: 708 sheet: 0.60 (0.29), residues: 308 loop : 0.01 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 72 TYR 0.026 0.002 TYR A 236 PHE 0.018 0.002 PHE D 164 TRP 0.014 0.001 TRP B 183 HIS 0.005 0.001 HIS D 218 Details of bonding type rmsd covalent geometry : bond 0.00343 (17084) covalent geometry : angle 0.60668 (23312) hydrogen bonds : bond 0.04935 ( 680) hydrogen bonds : angle 6.04738 ( 1872) Misc. bond : bond 0.06279 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.576 Fit side-chains REVERT: A 23 LYS cc_start: 0.8108 (ttpp) cc_final: 0.7850 (tttp) REVERT: A 128 ASP cc_start: 0.8932 (OUTLIER) cc_final: 0.8719 (m-30) REVERT: A 256 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7913 (mt-10) REVERT: A 273 LYS cc_start: 0.8764 (mttp) cc_final: 0.8520 (mtpt) REVERT: B 23 LYS cc_start: 0.8120 (ttpp) cc_final: 0.7862 (tttp) REVERT: B 128 ASP cc_start: 0.8934 (OUTLIER) cc_final: 0.8717 (m-30) REVERT: B 256 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7923 (mt-10) REVERT: B 273 LYS cc_start: 0.8764 (mttp) cc_final: 0.8521 (mtpt) REVERT: C 23 LYS cc_start: 0.8116 (ttpp) cc_final: 0.7853 (tttp) REVERT: C 128 ASP cc_start: 0.8932 (OUTLIER) cc_final: 0.8718 (m-30) REVERT: C 256 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7922 (mt-10) REVERT: C 273 LYS cc_start: 0.8763 (mttp) cc_final: 0.8518 (mtpt) REVERT: D 23 LYS cc_start: 0.8122 (ttpp) cc_final: 0.7861 (tttp) REVERT: D 59 ASP cc_start: 0.9115 (t70) cc_final: 0.8908 (t70) REVERT: D 128 ASP cc_start: 0.8925 (OUTLIER) cc_final: 0.8712 (m-30) REVERT: D 256 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7927 (mt-10) REVERT: D 273 LYS cc_start: 0.8753 (mttp) cc_final: 0.8508 (mtpt) outliers start: 20 outliers final: 4 residues processed: 136 average time/residue: 0.8279 time to fit residues: 122.8502 Evaluate side-chains 131 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 256 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 63 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 144 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 184 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN B 18 GLN C 18 GLN D 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.095751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.074528 restraints weight = 42366.733| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 1.69 r_work: 0.2643 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2526 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2526 r_free = 0.2526 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2526 r_free = 0.2526 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 17088 Z= 0.169 Angle : 0.628 6.310 23312 Z= 0.322 Chirality : 0.047 0.166 2352 Planarity : 0.005 0.040 3092 Dihedral : 9.095 101.908 2280 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.39 % Allowed : 7.04 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.18), residues: 2012 helix: 1.20 (0.20), residues: 712 sheet: 0.56 (0.30), residues: 308 loop : 0.03 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 156 TYR 0.028 0.002 TYR C 236 PHE 0.018 0.002 PHE C 57 TRP 0.014 0.002 TRP B 183 HIS 0.007 0.001 HIS C 218 Details of bonding type rmsd covalent geometry : bond 0.00401 (17084) covalent geometry : angle 0.62775 (23312) hydrogen bonds : bond 0.05231 ( 680) hydrogen bonds : angle 6.06918 ( 1872) Misc. bond : bond 0.08400 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.657 Fit side-chains REVERT: A 23 LYS cc_start: 0.8082 (ttpp) cc_final: 0.7868 (tttp) REVERT: A 128 ASP cc_start: 0.8992 (OUTLIER) cc_final: 0.8785 (m-30) REVERT: A 256 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7918 (mt-10) REVERT: A 273 LYS cc_start: 0.8876 (mttp) cc_final: 0.8570 (mtpt) REVERT: A 454 GLU cc_start: 0.7872 (mp0) cc_final: 0.7663 (mp0) REVERT: A 484 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: B 23 LYS cc_start: 0.8090 (ttpp) cc_final: 0.7880 (tttp) REVERT: B 128 ASP cc_start: 0.8999 (OUTLIER) cc_final: 0.8790 (m-30) REVERT: B 256 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7925 (mt-10) REVERT: B 273 LYS cc_start: 0.8877 (mttp) cc_final: 0.8569 (mtpt) REVERT: B 454 GLU cc_start: 0.7876 (mp0) cc_final: 0.7668 (mp0) REVERT: B 484 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: C 23 LYS cc_start: 0.8079 (ttpp) cc_final: 0.7867 (tttp) REVERT: C 128 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8791 (m-30) REVERT: C 256 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7921 (mt-10) REVERT: C 273 LYS cc_start: 0.8872 (mttp) cc_final: 0.8563 (mtpt) REVERT: C 454 GLU cc_start: 0.7881 (mp0) cc_final: 0.7671 (mp0) REVERT: C 484 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8129 (mt-10) REVERT: D 128 ASP cc_start: 0.8990 (OUTLIER) cc_final: 0.8787 (m-30) REVERT: D 256 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7934 (mt-10) REVERT: D 273 LYS cc_start: 0.8861 (mttp) cc_final: 0.8553 (mtpt) REVERT: D 454 GLU cc_start: 0.7868 (mp0) cc_final: 0.7656 (mp0) REVERT: D 484 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8116 (mt-10) outliers start: 24 outliers final: 8 residues processed: 136 average time/residue: 0.8051 time to fit residues: 120.1716 Evaluate side-chains 140 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 484 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 97 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 chunk 14 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 178 optimal weight: 20.0000 chunk 192 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN B 18 GLN C 18 GLN D 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.097046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.075933 restraints weight = 44356.326| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 1.72 r_work: 0.2673 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2554 r_free = 0.2554 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2554 r_free = 0.2554 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17088 Z= 0.138 Angle : 0.584 5.580 23312 Z= 0.298 Chirality : 0.045 0.166 2352 Planarity : 0.004 0.040 3092 Dihedral : 8.613 98.287 2280 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.39 % Allowed : 7.39 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.86 (0.19), residues: 2012 helix: 1.33 (0.20), residues: 712 sheet: 0.62 (0.30), residues: 308 loop : 0.09 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 156 TYR 0.025 0.002 TYR C 236 PHE 0.015 0.002 PHE C 136 TRP 0.012 0.001 TRP B 183 HIS 0.006 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00328 (17084) covalent geometry : angle 0.58429 (23312) hydrogen bonds : bond 0.04663 ( 680) hydrogen bonds : angle 5.93540 ( 1872) Misc. bond : bond 0.06032 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.706 Fit side-chains REVERT: A 128 ASP cc_start: 0.8937 (OUTLIER) cc_final: 0.8724 (m-30) REVERT: A 256 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7890 (mt-10) REVERT: A 273 LYS cc_start: 0.8835 (mttp) cc_final: 0.8541 (mtpt) REVERT: A 454 GLU cc_start: 0.7867 (mp0) cc_final: 0.7655 (mp0) REVERT: A 484 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8089 (mt-10) REVERT: B 128 ASP cc_start: 0.8951 (OUTLIER) cc_final: 0.8737 (m-30) REVERT: B 256 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7896 (mt-10) REVERT: B 273 LYS cc_start: 0.8835 (mttp) cc_final: 0.8538 (mtpt) REVERT: B 454 GLU cc_start: 0.7860 (mp0) cc_final: 0.7649 (mp0) REVERT: B 484 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8094 (mt-10) REVERT: C 128 ASP cc_start: 0.8950 (OUTLIER) cc_final: 0.8738 (m-30) REVERT: C 256 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7886 (mt-10) REVERT: C 273 LYS cc_start: 0.8830 (mttp) cc_final: 0.8534 (mtpt) REVERT: C 454 GLU cc_start: 0.7867 (mp0) cc_final: 0.7655 (mp0) REVERT: C 484 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: D 128 ASP cc_start: 0.8947 (OUTLIER) cc_final: 0.8738 (m-30) REVERT: D 256 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7887 (mt-10) REVERT: D 273 LYS cc_start: 0.8814 (mttp) cc_final: 0.8518 (mtpt) REVERT: D 454 GLU cc_start: 0.7853 (mp0) cc_final: 0.7641 (mp0) REVERT: D 484 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8102 (mt-10) outliers start: 24 outliers final: 8 residues processed: 133 average time/residue: 0.7742 time to fit residues: 113.0616 Evaluate side-chains 141 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 484 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 163 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 99 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 151 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 162 optimal weight: 0.8980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN B 18 GLN C 18 GLN D 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.096949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.075714 restraints weight = 46584.667| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 1.76 r_work: 0.2667 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2547 r_free = 0.2547 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2547 r_free = 0.2547 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 17088 Z= 0.143 Angle : 0.589 5.542 23312 Z= 0.300 Chirality : 0.045 0.166 2352 Planarity : 0.004 0.041 3092 Dihedral : 8.675 99.278 2280 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.62 % Allowed : 7.74 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.82 (0.19), residues: 2012 helix: 1.30 (0.20), residues: 712 sheet: 0.57 (0.30), residues: 308 loop : 0.08 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 156 TYR 0.025 0.002 TYR C 236 PHE 0.016 0.002 PHE A 136 TRP 0.013 0.001 TRP B 183 HIS 0.006 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00339 (17084) covalent geometry : angle 0.58910 (23312) hydrogen bonds : bond 0.04758 ( 680) hydrogen bonds : angle 5.93839 ( 1872) Misc. bond : bond 0.06362 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.458 Fit side-chains REVERT: A 128 ASP cc_start: 0.8969 (OUTLIER) cc_final: 0.8758 (m-30) REVERT: A 256 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7888 (mt-10) REVERT: A 273 LYS cc_start: 0.8832 (mttp) cc_final: 0.8541 (mtpt) REVERT: A 454 GLU cc_start: 0.7881 (mp0) cc_final: 0.7668 (mp0) REVERT: A 484 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8127 (mt-10) REVERT: B 128 ASP cc_start: 0.8969 (OUTLIER) cc_final: 0.8751 (m-30) REVERT: B 256 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7904 (mt-10) REVERT: B 273 LYS cc_start: 0.8834 (mttp) cc_final: 0.8541 (mtpt) REVERT: B 454 GLU cc_start: 0.7876 (mp0) cc_final: 0.7672 (mp0) REVERT: B 484 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8133 (mt-10) REVERT: C 128 ASP cc_start: 0.8960 (OUTLIER) cc_final: 0.8747 (m-30) REVERT: C 256 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7899 (mt-10) REVERT: C 273 LYS cc_start: 0.8827 (mttp) cc_final: 0.8533 (mtpt) REVERT: C 454 GLU cc_start: 0.7895 (mp0) cc_final: 0.7680 (mp0) REVERT: C 484 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8153 (mt-10) REVERT: D 124 ASP cc_start: 0.8882 (m-30) cc_final: 0.8595 (m-30) REVERT: D 128 ASP cc_start: 0.8953 (OUTLIER) cc_final: 0.8741 (m-30) REVERT: D 256 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7890 (mt-10) REVERT: D 273 LYS cc_start: 0.8822 (mttp) cc_final: 0.8530 (mtpt) REVERT: D 454 GLU cc_start: 0.7877 (mp0) cc_final: 0.7661 (mp0) REVERT: D 484 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8145 (mt-10) outliers start: 28 outliers final: 8 residues processed: 137 average time/residue: 0.8160 time to fit residues: 122.4598 Evaluate side-chains 141 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 484 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 166 optimal weight: 7.9990 chunk 125 optimal weight: 0.0270 chunk 40 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 198 optimal weight: 5.9990 chunk 150 optimal weight: 0.0050 chunk 35 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 overall best weight: 3.8058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN B 18 GLN C 18 GLN D 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.096656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.075702 restraints weight = 43031.539| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 1.69 r_work: 0.2669 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2549 r_free = 0.2549 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2549 r_free = 0.2549 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 17088 Z= 0.153 Angle : 0.599 5.575 23312 Z= 0.305 Chirality : 0.045 0.166 2352 Planarity : 0.004 0.043 3092 Dihedral : 8.782 100.765 2280 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.15 % Allowed : 8.26 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.84 (0.19), residues: 2012 helix: 1.29 (0.20), residues: 712 sheet: 0.58 (0.31), residues: 304 loop : 0.13 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 156 TYR 0.025 0.002 TYR C 236 PHE 0.017 0.002 PHE B 136 TRP 0.013 0.001 TRP B 183 HIS 0.007 0.001 HIS D 218 Details of bonding type rmsd covalent geometry : bond 0.00363 (17084) covalent geometry : angle 0.59929 (23312) hydrogen bonds : bond 0.04890 ( 680) hydrogen bonds : angle 5.97088 ( 1872) Misc. bond : bond 0.06848 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.609 Fit side-chains REVERT: A 128 ASP cc_start: 0.8967 (OUTLIER) cc_final: 0.8757 (m-30) REVERT: A 256 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7889 (mt-10) REVERT: A 273 LYS cc_start: 0.8835 (mttp) cc_final: 0.8548 (mtpt) REVERT: A 454 GLU cc_start: 0.7859 (mp0) cc_final: 0.7658 (mp0) REVERT: A 484 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8115 (mt-10) REVERT: B 128 ASP cc_start: 0.8967 (OUTLIER) cc_final: 0.8751 (m-30) REVERT: B 256 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7893 (mt-10) REVERT: B 273 LYS cc_start: 0.8832 (mttp) cc_final: 0.8544 (mtpt) REVERT: B 454 GLU cc_start: 0.7866 (mp0) cc_final: 0.7666 (mp0) REVERT: B 484 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8123 (mt-10) REVERT: C 128 ASP cc_start: 0.8974 (OUTLIER) cc_final: 0.8763 (m-30) REVERT: C 256 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7895 (mt-10) REVERT: C 273 LYS cc_start: 0.8827 (mttp) cc_final: 0.8537 (mtpt) REVERT: C 454 GLU cc_start: 0.7872 (mp0) cc_final: 0.7669 (mp0) REVERT: C 484 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8133 (mt-10) REVERT: D 128 ASP cc_start: 0.8971 (OUTLIER) cc_final: 0.8761 (m-30) REVERT: D 256 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7893 (mt-10) REVERT: D 273 LYS cc_start: 0.8817 (mttp) cc_final: 0.8527 (mtpt) REVERT: D 454 GLU cc_start: 0.7855 (mp0) cc_final: 0.7652 (mp0) REVERT: D 484 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8127 (mt-10) outliers start: 20 outliers final: 8 residues processed: 136 average time/residue: 0.8165 time to fit residues: 121.6841 Evaluate side-chains 140 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 484 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 139 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 80 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN B 18 GLN C 18 GLN D 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.096465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.075592 restraints weight = 41998.154| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 1.68 r_work: 0.2668 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2549 r_free = 0.2549 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2549 r_free = 0.2549 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 17088 Z= 0.158 Angle : 0.606 5.683 23312 Z= 0.307 Chirality : 0.046 0.166 2352 Planarity : 0.004 0.043 3092 Dihedral : 8.814 101.319 2280 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.33 % Allowed : 8.26 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.82 (0.19), residues: 2012 helix: 1.28 (0.20), residues: 712 sheet: 0.66 (0.31), residues: 284 loop : 0.08 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 156 TYR 0.026 0.002 TYR D 236 PHE 0.017 0.002 PHE A 136 TRP 0.013 0.001 TRP B 183 HIS 0.007 0.001 HIS C 218 Details of bonding type rmsd covalent geometry : bond 0.00378 (17084) covalent geometry : angle 0.60600 (23312) hydrogen bonds : bond 0.04929 ( 680) hydrogen bonds : angle 5.97490 ( 1872) Misc. bond : bond 0.07477 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.456 Fit side-chains REVERT: A 128 ASP cc_start: 0.8973 (OUTLIER) cc_final: 0.8764 (m-30) REVERT: A 256 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7887 (mt-10) REVERT: A 273 LYS cc_start: 0.8834 (mttp) cc_final: 0.8546 (mtpt) REVERT: A 454 GLU cc_start: 0.7863 (mp0) cc_final: 0.7661 (mp0) REVERT: A 484 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8089 (mt-10) REVERT: B 128 ASP cc_start: 0.8969 (OUTLIER) cc_final: 0.8753 (m-30) REVERT: B 256 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7895 (mt-10) REVERT: B 273 LYS cc_start: 0.8832 (mttp) cc_final: 0.8543 (mtpt) REVERT: B 454 GLU cc_start: 0.7867 (mp0) cc_final: 0.7666 (mp0) REVERT: B 484 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8089 (mt-10) REVERT: C 128 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8765 (m-30) REVERT: C 256 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7896 (mt-10) REVERT: C 273 LYS cc_start: 0.8826 (mttp) cc_final: 0.8534 (mtpt) REVERT: C 454 GLU cc_start: 0.7868 (mp0) cc_final: 0.7665 (mp0) REVERT: C 484 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8101 (mt-10) REVERT: D 128 ASP cc_start: 0.8974 (OUTLIER) cc_final: 0.8763 (m-30) REVERT: D 256 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7892 (mt-10) REVERT: D 273 LYS cc_start: 0.8816 (mttp) cc_final: 0.8524 (mtpt) REVERT: D 454 GLU cc_start: 0.7854 (mp0) cc_final: 0.7649 (mp0) REVERT: D 484 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8097 (mt-10) outliers start: 23 outliers final: 11 residues processed: 132 average time/residue: 0.7887 time to fit residues: 114.0810 Evaluate side-chains 143 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 382 ARG Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 382 ARG Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 382 ARG Chi-restraints excluded: chain D residue 484 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 134 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 197 optimal weight: 20.0000 chunk 108 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 174 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 193 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN B 18 GLN C 18 GLN D 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.096520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.076950 restraints weight = 28645.156| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 1.39 r_work: 0.2699 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2584 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2584 r_free = 0.2584 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2584 r_free = 0.2584 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2584 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 17088 Z= 0.158 Angle : 0.605 5.652 23312 Z= 0.307 Chirality : 0.046 0.166 2352 Planarity : 0.004 0.043 3092 Dihedral : 8.819 101.567 2280 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.33 % Allowed : 8.03 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.83 (0.19), residues: 2012 helix: 1.29 (0.20), residues: 712 sheet: 0.67 (0.32), residues: 284 loop : 0.08 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 156 TYR 0.026 0.002 TYR C 236 PHE 0.017 0.002 PHE B 136 TRP 0.013 0.001 TRP B 183 HIS 0.007 0.001 HIS C 218 Details of bonding type rmsd covalent geometry : bond 0.00378 (17084) covalent geometry : angle 0.60540 (23312) hydrogen bonds : bond 0.04931 ( 680) hydrogen bonds : angle 5.97757 ( 1872) Misc. bond : bond 0.07301 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.668 Fit side-chains REVERT: A 128 ASP cc_start: 0.8930 (OUTLIER) cc_final: 0.8719 (m-30) REVERT: A 256 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7880 (mt-10) REVERT: A 273 LYS cc_start: 0.8809 (mttp) cc_final: 0.8529 (mtpt) REVERT: A 484 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8036 (mt-10) REVERT: B 128 ASP cc_start: 0.8924 (OUTLIER) cc_final: 0.8709 (m-30) REVERT: B 256 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7890 (mt-10) REVERT: B 273 LYS cc_start: 0.8812 (mttp) cc_final: 0.8531 (mtpt) REVERT: B 484 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8041 (mt-10) REVERT: C 128 ASP cc_start: 0.8932 (OUTLIER) cc_final: 0.8719 (m-30) REVERT: C 256 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7885 (mt-10) REVERT: C 273 LYS cc_start: 0.8805 (mttp) cc_final: 0.8523 (mtpt) REVERT: C 484 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8059 (mt-10) REVERT: D 124 ASP cc_start: 0.8876 (m-30) cc_final: 0.8603 (m-30) REVERT: D 128 ASP cc_start: 0.8931 (OUTLIER) cc_final: 0.8718 (m-30) REVERT: D 256 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7884 (mt-10) REVERT: D 273 LYS cc_start: 0.8796 (mttp) cc_final: 0.8514 (mtpt) REVERT: D 484 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8049 (mt-10) outliers start: 23 outliers final: 11 residues processed: 133 average time/residue: 0.7703 time to fit residues: 112.6721 Evaluate side-chains 144 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 382 ARG Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 382 ARG Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 382 ARG Chi-restraints excluded: chain D residue 484 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 85 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 55 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 chunk 157 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 7 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN B 18 GLN C 18 GLN D 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.095264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.074454 restraints weight = 41294.297| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 1.66 r_work: 0.2644 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2528 r_free = 0.2528 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2528 r_free = 0.2528 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 17088 Z= 0.205 Angle : 0.659 6.821 23312 Z= 0.337 Chirality : 0.048 0.167 2352 Planarity : 0.005 0.047 3092 Dihedral : 9.357 108.038 2280 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.39 % Allowed : 7.74 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.65 (0.18), residues: 2012 helix: 1.12 (0.20), residues: 712 sheet: 0.56 (0.31), residues: 284 loop : -0.00 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 156 TYR 0.028 0.002 TYR C 236 PHE 0.020 0.003 PHE A 136 TRP 0.013 0.002 TRP B 183 HIS 0.007 0.002 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00494 (17084) covalent geometry : angle 0.65880 (23312) hydrogen bonds : bond 0.05551 ( 680) hydrogen bonds : angle 6.11256 ( 1872) Misc. bond : bond 0.08601 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.619 Fit side-chains REVERT: A 256 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7926 (mt-10) REVERT: A 273 LYS cc_start: 0.8861 (mttp) cc_final: 0.8578 (mtpt) REVERT: A 454 GLU cc_start: 0.8034 (mp0) cc_final: 0.7821 (mp0) REVERT: A 484 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8095 (mt-10) REVERT: B 128 ASP cc_start: 0.9013 (OUTLIER) cc_final: 0.8810 (m-30) REVERT: B 256 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7932 (mt-10) REVERT: B 273 LYS cc_start: 0.8860 (mttp) cc_final: 0.8574 (mtpt) REVERT: B 454 GLU cc_start: 0.8029 (mp0) cc_final: 0.7818 (mp0) REVERT: B 484 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8098 (mt-10) REVERT: C 128 ASP cc_start: 0.9008 (OUTLIER) cc_final: 0.8807 (m-30) REVERT: C 256 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7933 (mt-10) REVERT: C 273 LYS cc_start: 0.8852 (mttp) cc_final: 0.8564 (mtpt) REVERT: C 454 GLU cc_start: 0.8034 (mp0) cc_final: 0.7823 (mp0) REVERT: C 484 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8110 (mt-10) REVERT: D 256 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7934 (mt-10) REVERT: D 273 LYS cc_start: 0.8844 (mttp) cc_final: 0.8556 (mtpt) REVERT: D 454 GLU cc_start: 0.8020 (mp0) cc_final: 0.7814 (mp0) REVERT: D 484 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8117 (mt-10) outliers start: 24 outliers final: 12 residues processed: 136 average time/residue: 0.7340 time to fit residues: 109.9106 Evaluate side-chains 144 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 382 ARG Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 382 ARG Chi-restraints excluded: chain C residue 484 GLU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 382 ARG Chi-restraints excluded: chain D residue 484 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 74 optimal weight: 9.9990 chunk 144 optimal weight: 0.8980 chunk 187 optimal weight: 0.0370 chunk 72 optimal weight: 5.9990 chunk 80 optimal weight: 0.0980 chunk 141 optimal weight: 7.9990 chunk 186 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 179 optimal weight: 7.9990 chunk 13 optimal weight: 0.0170 chunk 135 optimal weight: 0.6980 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN B 18 GLN C 18 GLN D 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.103750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.083830 restraints weight = 36499.438| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.58 r_work: 0.2822 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17088 Z= 0.095 Angle : 0.534 5.515 23312 Z= 0.266 Chirality : 0.042 0.167 2352 Planarity : 0.004 0.037 3092 Dihedral : 7.462 89.815 2280 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.75 % Allowed : 8.60 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.18 (0.19), residues: 2012 helix: 1.58 (0.20), residues: 712 sheet: 0.94 (0.31), residues: 300 loop : 0.25 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 127 TYR 0.018 0.001 TYR D 500 PHE 0.010 0.001 PHE A 409 TRP 0.008 0.001 TRP B 183 HIS 0.002 0.001 HIS C 235 Details of bonding type rmsd covalent geometry : bond 0.00229 (17084) covalent geometry : angle 0.53379 (23312) hydrogen bonds : bond 0.03389 ( 680) hydrogen bonds : angle 5.57982 ( 1872) Misc. bond : bond 0.00377 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6745.31 seconds wall clock time: 115 minutes 30.03 seconds (6930.03 seconds total)