Starting phenix.real_space_refine on Sun Aug 24 06:53:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8el9_28225/08_2025/8el9_28225.cif Found real_map, /net/cci-nas-00/data/ceres_data/8el9_28225/08_2025/8el9_28225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8el9_28225/08_2025/8el9_28225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8el9_28225/08_2025/8el9_28225.map" model { file = "/net/cci-nas-00/data/ceres_data/8el9_28225/08_2025/8el9_28225.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8el9_28225/08_2025/8el9_28225.cif" } resolution = 2.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.113 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 64 atoms to isotropic. 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 10420 2.51 5 N 2899 2.21 5 O 4042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17429 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 497, 3997 Classifications: {'peptide': 497} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 497, 3997 Classifications: {'peptide': 497} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 4102 Chain: "B" Number of atoms: 4009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 497, 3997 Classifications: {'peptide': 497} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 497, 3997 Classifications: {'peptide': 497} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 4102 Chain: "C" Number of atoms: 4018 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 498, 4006 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} Conformer: "B" Number of residues, atoms: 498, 4006 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} bond proxies already assigned to first conformer: 4111 Chain: "D" Number of atoms: 4014 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 498, 4002 Classifications: {'peptide': 498} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 498, 4002 Classifications: {'peptide': 498} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 4107 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: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 257 Classifications: {'water': 257} Link IDs: {None: 256} Chain: "B" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 260 Classifications: {'water': 260} Link IDs: {None: 259} Chain: "C" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 244 Classifications: {'water': 244} Link IDs: {None: 243} Chain: "D" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 254 Classifications: {'water': 254} Link IDs: {None: 253} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AGLY A 121 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 121 " occ=0.50 residue: pdb=" N AGLY B 121 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY B 121 " occ=0.50 residue: pdb=" N AGLY C 121 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY C 121 " occ=0.50 residue: pdb=" N AGLY D 121 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY D 121 " occ=0.50 Time building chain proxies: 6.48, per 1000 atoms: 0.37 Number of scatterers: 17429 At special positions: 0 Unit cell: (85.32, 113.4, 109.08, 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 4042 8.00 N 2899 7.00 C 10420 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: 1.30 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 1.2 microseconds 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3724 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 8 sheets defined 39.0% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 10 through 19 Processing helix chain 'A' and resid 54 through 66 removed outlier: 3.536A pdb=" N HIS A 63 " --> pdb=" O ASP A 59 " (cutoff:3.500A) 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 200 Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 246 through 257 removed outlier: 3.674A 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 291 removed outlier: 3.543A pdb=" N THR A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 348 through 366 removed outlier: 3.891A pdb=" N PHE A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR A 358 " --> pdb=" O ARG A 354 " (cutoff:3.500A) Proline residue: A 359 - end of helix removed outlier: 3.550A pdb=" N HIS A 364 " --> pdb=" O ASP A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 373 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 Processing helix chain 'A' and resid 486 through 501 Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 54 through 66 removed outlier: 3.621A pdb=" N HIS B 63 " --> pdb=" O ASP B 59 " (cutoff:3.500A) 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 168 Processing helix chain 'B' and resid 178 through 189 Processing helix chain 'B' and resid 192 through 200 Processing helix chain 'B' and resid 201 through 205 removed outlier: 3.558A pdb=" N ILE B 205 " --> pdb=" O ASP B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 257 removed outlier: 3.583A 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 291 removed outlier: 3.751A pdb=" N GLU B 290 " --> pdb=" O PHE B 286 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR B 291 " --> pdb=" O ASN B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 348 through 366 removed outlier: 3.847A pdb=" N PHE B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR B 358 " --> pdb=" O ARG B 354 " (cutoff:3.500A) Proline residue: B 359 - end of helix removed outlier: 3.536A pdb=" N HIS B 364 " --> pdb=" O ASP B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 373 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 Processing helix chain 'B' and resid 486 through 501 Processing helix chain 'C' and resid 10 through 19 Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.599A pdb=" N HIS C 63 " --> pdb=" O ASP C 59 " (cutoff:3.500A) 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 168 Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'C' and resid 192 through 200 Processing helix chain 'C' and resid 201 through 205 removed outlier: 3.593A pdb=" N ILE C 205 " --> pdb=" O ASP C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 257 removed outlier: 3.722A 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: 3.838A pdb=" N PHE C 356 " --> pdb=" O GLN C 352 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR C 358 " --> pdb=" O ARG C 354 " (cutoff:3.500A) Proline residue: C 359 - end of helix Processing helix chain 'C' and resid 369 through 373 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 Processing helix chain 'C' and resid 486 through 502 removed outlier: 3.546A pdb=" N ALA C 502 " --> pdb=" O ASP C 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 19 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 200 Processing helix chain 'D' and resid 201 through 205 removed outlier: 3.549A pdb=" N ILE D 205 " --> pdb=" O ASP D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 257 removed outlier: 3.706A 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: 3.837A pdb=" N PHE D 356 " --> pdb=" O GLN D 352 " (cutoff:3.500A) Proline residue: D 359 - end of helix removed outlier: 3.544A pdb=" N HIS D 364 " --> pdb=" O ASP D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 373 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 Processing helix chain 'D' and resid 486 through 502 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 44 removed outlier: 3.567A pdb=" N ARG C 430 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE B 423 " --> pdb=" O VAL C 429 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 343 through 345 removed outlier: 6.387A pdb=" N TRP A 277 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS A 315 " --> pdb=" O TRP A 277 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N PHE A 279 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE A 82 " --> pdb=" O ASN A 319 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 423 through 424 removed outlier: 4.098A pdb=" N ILE A 423 " --> pdb=" O VAL D 429 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 44 removed outlier: 4.063A pdb=" N ILE D 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: 5.963A pdb=" N ILE B 281 " --> pdb=" O PRO B 312 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE B 82 " --> pdb=" O ASN B 319 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 423 through 424 removed outlier: 3.859A pdb=" N ILE C 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: 8.334A pdb=" N GLY C 214 " --> pdb=" O THR C 238 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N THR C 238 " --> pdb=" O GLY C 214 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N GLY C 216 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N TYR C 236 " --> pdb=" O GLY C 216 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N HIS C 218 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N PHE C 234 " --> pdb=" O HIS C 218 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TRP C 277 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS C 315 " --> pdb=" O TRP C 277 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE C 279 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE C 82 " --> pdb=" O ASN C 319 " (cutoff:3.500A) removed outlier: 15.274A pdb=" N ASN C 142 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 14.411A pdb=" N LYS C 221 " --> pdb=" O ASN C 142 " (cutoff:3.500A) removed outlier: 13.452A pdb=" N ASP C 144 " --> pdb=" O THR C 219 " (cutoff:3.500A) removed outlier: 11.940A pdb=" N THR C 219 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 10.714A pdb=" N VAL C 146 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N SER C 217 " --> pdb=" O VAL C 146 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 343 through 345 removed outlier: 6.448A pdb=" N TRP D 277 " --> pdb=" O LYS D 315 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS D 315 " --> pdb=" O TRP D 277 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE D 279 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N PHE D 82 " --> pdb=" O ASN D 319 " (cutoff:3.500A) 663 hydrogen bonds defined for protein. 1847 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: 2.48 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 7281 1.39 - 1.56: 9529 1.56 - 1.73: 20 1.73 - 1.90: 96 1.90 - 2.06: 16 Bond restraints: 16942 Sorted by residual: bond pdb=" CA GLN D 395 " pdb=" CB GLN D 395 " ideal model delta sigma weight residual 1.537 1.519 0.017 1.45e-02 4.76e+03 1.42e+00 bond pdb=" N GLY D 314 " pdb=" CA GLY D 314 " ideal model delta sigma weight residual 1.458 1.447 0.010 9.20e-03 1.18e+04 1.29e+00 bond pdb=" CA GLN B 395 " pdb=" C GLN B 395 " ideal model delta sigma weight residual 1.524 1.517 0.008 7.00e-03 2.04e+04 1.16e+00 bond pdb=" C GLN B 395 " pdb=" O GLN B 395 " ideal model delta sigma weight residual 1.233 1.247 -0.014 1.32e-02 5.74e+03 1.06e+00 bond pdb=" CA TYR D 358 " pdb=" C TYR D 358 " ideal model delta sigma weight residual 1.524 1.536 -0.013 1.26e-02 6.30e+03 9.98e-01 ... (remaining 16937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 22464 1.62 - 3.24: 505 3.24 - 4.86: 109 4.86 - 6.48: 41 6.48 - 8.10: 4 Bond angle restraints: 23123 Sorted by residual: angle pdb=" C ASP C 389 " pdb=" CA ASP C 389 " pdb=" CB ASP C 389 " ideal model delta sigma weight residual 115.89 109.79 6.10 1.32e+00 5.74e-01 2.14e+01 angle pdb=" C MET B 394 " pdb=" N GLN B 395 " pdb=" CA GLN B 395 " ideal model delta sigma weight residual 122.44 117.97 4.47 1.19e+00 7.06e-01 1.41e+01 angle pdb=" N GLY D 314 " pdb=" CA GLY D 314 " pdb=" C GLY D 314 " ideal model delta sigma weight residual 111.16 117.00 -5.84 1.76e+00 3.23e-01 1.10e+01 angle pdb=" C VAL D 313 " pdb=" N GLY D 314 " pdb=" CA GLY D 314 " ideal model delta sigma weight residual 122.16 119.76 2.40 7.70e-01 1.69e+00 9.71e+00 angle pdb=" N GLY C 216 " pdb=" CA GLY C 216 " pdb=" C GLY C 216 " ideal model delta sigma weight residual 113.18 105.94 7.24 2.37e+00 1.78e-01 9.33e+00 ... (remaining 23118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.52: 8817 20.52 - 41.03: 849 41.03 - 61.55: 171 61.55 - 82.06: 55 82.06 - 102.58: 9 Dihedral angle restraints: 9901 sinusoidal: 4091 harmonic: 5810 Sorted by residual: dihedral pdb=" CA HIS A 372 " pdb=" C HIS A 372 " pdb=" N ILE A 373 " pdb=" CA ILE A 373 " ideal model delta harmonic sigma weight residual 180.00 155.18 24.82 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA HIS D 372 " pdb=" C HIS D 372 " pdb=" N ILE D 373 " pdb=" CA ILE D 373 " ideal model delta harmonic sigma weight residual 180.00 155.54 24.46 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA HIS B 372 " pdb=" C HIS B 372 " pdb=" N ILE B 373 " pdb=" CA ILE B 373 " ideal model delta harmonic sigma weight residual 180.00 155.93 24.07 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 9898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1446 0.036 - 0.073: 607 0.073 - 0.109: 225 0.109 - 0.145: 52 0.145 - 0.181: 4 Chirality restraints: 2334 Sorted by residual: chirality pdb=" CA ILE D 373 " pdb=" N ILE D 373 " pdb=" C ILE D 373 " pdb=" CB ILE D 373 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.23e-01 chirality pdb=" CA ILE B 373 " pdb=" N ILE B 373 " pdb=" C ILE B 373 " pdb=" CB ILE B 373 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" CA ILE A 373 " pdb=" N ILE A 373 " pdb=" C ILE A 373 " pdb=" CB ILE A 373 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.60e-01 ... (remaining 2331 not shown) Planarity restraints: 3067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 346 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO C 347 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 347 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 347 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 346 " -0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO B 347 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 347 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 347 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 346 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO A 347 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 347 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 347 " 0.026 5.00e-02 4.00e+02 ... (remaining 3064 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1464 2.74 - 3.28: 17108 3.28 - 3.82: 35033 3.82 - 4.36: 44663 4.36 - 4.90: 67684 Nonbonded interactions: 165952 Sorted by model distance: nonbonded pdb=" O LYS A 273 " pdb=" O HOH A 701 " model vdw 2.197 3.040 nonbonded pdb=" O HOH D 747 " pdb=" O HOH D 872 " model vdw 2.223 3.040 nonbonded pdb=" O HOH B 715 " pdb=" O HOH B 737 " model vdw 2.229 3.040 nonbonded pdb=" O HOH C 765 " pdb=" O HOH C 876 " model vdw 2.234 3.040 nonbonded pdb=" O HOH D 713 " pdb=" O HOH D 779 " model vdw 2.245 3.040 ... (remaining 165947 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 18 or resid 20 through 120 or resid 122 through \ 602)) selection = (chain 'B' and (resid 5 through 18 or resid 20 through 120 or resid 122 through \ 602)) selection = (chain 'C' and (resid 5 through 18 or resid 20 through 120 or resid 122 through \ 394 or (resid 395 and (name N or name CA or name C or name O or name CB )) or re \ sid 396 through 501 or resid 601 through 602)) selection = (chain 'D' and (resid 5 through 18 or resid 20 through 120 or resid 122 through \ 501 or resid 601 through 602)) } 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: 4.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.720 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 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 : 0.003 0.055 16946 Z= 0.138 Angle : 0.652 8.096 23123 Z= 0.337 Chirality : 0.046 0.181 2334 Planarity : 0.005 0.048 3067 Dihedral : 17.091 102.575 6177 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.23 % Allowed : 13.43 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: 0.05 (0.18), residues: 1998 helix: 0.50 (0.19), residues: 702 sheet: 0.65 (0.31), residues: 290 loop : -0.41 (0.18), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 252 TYR 0.031 0.002 TYR C 236 PHE 0.012 0.002 PHE C 473 TRP 0.012 0.002 TRP A 183 HIS 0.005 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00298 (16942) covalent geometry : angle 0.65210 (23123) hydrogen bonds : bond 0.16963 ( 663) hydrogen bonds : angle 8.01266 ( 1847) Misc. bond : bond 0.01432 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 0.531 Fit side-chains REVERT: A 499 LYS cc_start: 0.7604 (mtpp) cc_final: 0.7368 (mtmm) REVERT: C 476 LYS cc_start: 0.8140 (mmpt) cc_final: 0.7801 (mttt) outliers start: 19 outliers final: 18 residues processed: 199 average time/residue: 0.7090 time to fit residues: 155.3793 Evaluate side-chains 190 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 361 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.1980 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.0050 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN A 372 HIS A 449 ASN B 331 GLN B 372 HIS ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 HIS D 331 GLN D 372 HIS D 449 ASN D 501 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.120454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.105513 restraints weight = 36352.720| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.12 r_work: 0.3016 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.0776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 16946 Z= 0.113 Angle : 0.579 6.599 23123 Z= 0.300 Chirality : 0.045 0.166 2334 Planarity : 0.005 0.049 3067 Dihedral : 8.395 99.340 2298 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.05 % Allowed : 13.49 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: 0.38 (0.18), residues: 1998 helix: 0.69 (0.20), residues: 718 sheet: 1.12 (0.32), residues: 294 loop : -0.27 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 382 TYR 0.024 0.001 TYR C 236 PHE 0.013 0.002 PHE A 136 TRP 0.010 0.001 TRP B 183 HIS 0.004 0.001 HIS D 63 Details of bonding type rmsd covalent geometry : bond 0.00247 (16942) covalent geometry : angle 0.57945 (23123) hydrogen bonds : bond 0.04795 ( 663) hydrogen bonds : angle 6.17531 ( 1847) Misc. bond : bond 0.00946 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 0.746 Fit side-chains REVERT: A 306 LYS cc_start: 0.8087 (mptt) cc_final: 0.7778 (mtmm) REVERT: A 372 HIS cc_start: 0.7663 (m90) cc_final: 0.7434 (m170) REVERT: A 438 ASP cc_start: 0.8399 (t0) cc_final: 0.8167 (t0) REVERT: B 499 LYS cc_start: 0.8104 (mtpm) cc_final: 0.7685 (mtpp) REVERT: C 252 ARG cc_start: 0.8564 (ttp80) cc_final: 0.8307 (ttp80) REVERT: C 453 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7157 (mm-30) REVERT: C 476 LYS cc_start: 0.8368 (mmpt) cc_final: 0.7797 (mttt) outliers start: 16 outliers final: 10 residues processed: 200 average time/residue: 0.7438 time to fit residues: 164.8854 Evaluate side-chains 177 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 167 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 44 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 8 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 74 optimal weight: 0.0270 chunk 184 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 123 optimal weight: 0.4980 chunk 86 optimal weight: 0.9990 chunk 118 optimal weight: 8.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN A 449 ASN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN D 449 ASN D 501 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.118931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.104013 restraints weight = 36505.021| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.11 r_work: 0.2994 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16946 Z= 0.118 Angle : 0.590 6.756 23123 Z= 0.304 Chirality : 0.045 0.166 2334 Planarity : 0.005 0.049 3067 Dihedral : 8.309 99.673 2281 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.87 % Allowed : 12.32 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: 0.48 (0.19), residues: 1998 helix: 0.78 (0.20), residues: 718 sheet: 1.20 (0.32), residues: 294 loop : -0.23 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 382 TYR 0.025 0.002 TYR C 236 PHE 0.017 0.002 PHE C 136 TRP 0.010 0.001 TRP D 183 HIS 0.005 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00261 (16942) covalent geometry : angle 0.58952 (23123) hydrogen bonds : bond 0.04928 ( 663) hydrogen bonds : angle 6.01852 ( 1847) Misc. bond : bond 0.01635 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 0.741 Fit side-chains REVERT: A 124 ASP cc_start: 0.8872 (m-30) cc_final: 0.8664 (m-30) REVERT: A 372 HIS cc_start: 0.7515 (m90) cc_final: 0.7294 (m170) REVERT: A 438 ASP cc_start: 0.8437 (t0) cc_final: 0.8177 (t0) REVERT: C 453 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7188 (mm-30) outliers start: 30 outliers final: 18 residues processed: 196 average time/residue: 0.7208 time to fit residues: 156.5484 Evaluate side-chains 180 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 146 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 66 optimal weight: 0.6980 chunk 191 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 1 optimal weight: 0.0030 chunk 113 optimal weight: 0.0010 chunk 177 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN A 449 ASN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN D 449 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.119075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.104321 restraints weight = 35171.502| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.09 r_work: 0.3000 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16946 Z= 0.118 Angle : 0.589 6.738 23123 Z= 0.303 Chirality : 0.045 0.164 2334 Planarity : 0.005 0.049 3067 Dihedral : 8.316 99.783 2281 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.75 % Allowed : 12.55 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: 0.55 (0.19), residues: 1998 helix: 0.91 (0.20), residues: 706 sheet: 1.24 (0.32), residues: 294 loop : -0.23 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 252 TYR 0.025 0.002 TYR A 236 PHE 0.016 0.002 PHE A 136 TRP 0.010 0.001 TRP A 183 HIS 0.006 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00261 (16942) covalent geometry : angle 0.58889 (23123) hydrogen bonds : bond 0.04815 ( 663) hydrogen bonds : angle 5.95384 ( 1847) Misc. bond : bond 0.01691 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.598 Fit side-chains REVERT: A 124 ASP cc_start: 0.8865 (m-30) cc_final: 0.8656 (m-30) REVERT: C 453 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7225 (mm-30) REVERT: C 476 LYS cc_start: 0.8381 (mmpt) cc_final: 0.7810 (mttt) outliers start: 28 outliers final: 20 residues processed: 186 average time/residue: 0.6896 time to fit residues: 142.3472 Evaluate side-chains 180 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.4980 chunk 82 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 175 optimal weight: 0.0970 chunk 131 optimal weight: 2.9990 chunk 190 optimal weight: 0.0470 chunk 35 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN D 449 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.120738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.105927 restraints weight = 35936.886| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.10 r_work: 0.3022 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16946 Z= 0.107 Angle : 0.564 6.347 23123 Z= 0.289 Chirality : 0.044 0.160 2334 Planarity : 0.004 0.048 3067 Dihedral : 8.037 97.092 2281 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.52 % Allowed : 12.84 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: 0.63 (0.19), residues: 1998 helix: 0.96 (0.20), residues: 704 sheet: 1.28 (0.32), residues: 294 loop : -0.18 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 252 TYR 0.021 0.001 TYR C 236 PHE 0.015 0.002 PHE B 136 TRP 0.010 0.001 TRP A 183 HIS 0.004 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00238 (16942) covalent geometry : angle 0.56407 (23123) hydrogen bonds : bond 0.04416 ( 663) hydrogen bonds : angle 5.81636 ( 1847) Misc. bond : bond 0.01253 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.568 Fit side-chains REVERT: A 315 LYS cc_start: 0.8883 (ptmm) cc_final: 0.8547 (pttm) REVERT: A 499 LYS cc_start: 0.7691 (mtpp) cc_final: 0.7463 (mtpm) REVERT: C 12 MET cc_start: 0.8809 (mtm) cc_final: 0.8557 (mtm) REVERT: C 453 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7168 (mm-30) REVERT: C 476 LYS cc_start: 0.8374 (mmpt) cc_final: 0.7818 (mttt) REVERT: D 237 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8034 (mmtm) REVERT: D 453 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7128 (mm-30) outliers start: 24 outliers final: 17 residues processed: 185 average time/residue: 0.6586 time to fit residues: 135.2176 Evaluate side-chains 183 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 237 LYS Chi-restraints excluded: chain D residue 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 96 optimal weight: 4.9990 chunk 120 optimal weight: 0.0970 chunk 186 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN C 235 HIS ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN D 449 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.115790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.100851 restraints weight = 36388.257| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.10 r_work: 0.2951 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2854 r_free = 0.2854 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16946 Z= 0.164 Angle : 0.669 7.947 23123 Z= 0.346 Chirality : 0.048 0.163 2334 Planarity : 0.005 0.052 3067 Dihedral : 8.763 104.499 2281 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.58 % Allowed : 12.67 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: 0.36 (0.18), residues: 1998 helix: 0.77 (0.20), residues: 712 sheet: 0.99 (0.32), residues: 294 loop : -0.32 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 382 TYR 0.030 0.002 TYR C 236 PHE 0.018 0.003 PHE A 136 TRP 0.011 0.002 TRP D 183 HIS 0.008 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00363 (16942) covalent geometry : angle 0.66917 (23123) hydrogen bonds : bond 0.05896 ( 663) hydrogen bonds : angle 6.20334 ( 1847) Misc. bond : bond 0.03306 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.606 Fit side-chains REVERT: B 457 LYS cc_start: 0.8446 (tttp) cc_final: 0.7723 (ttpt) REVERT: C 124 ASP cc_start: 0.8838 (m-30) cc_final: 0.8610 (m-30) REVERT: C 236 TYR cc_start: 0.9102 (OUTLIER) cc_final: 0.8715 (p90) REVERT: D 237 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.7829 (mmtm) REVERT: D 453 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7208 (mm-30) outliers start: 25 outliers final: 17 residues processed: 188 average time/residue: 0.6595 time to fit residues: 137.2752 Evaluate side-chains 185 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 237 LYS Chi-restraints excluded: chain D residue 361 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 73 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN B 287 ASN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN C 501 ASN D 449 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.117652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.104306 restraints weight = 24318.121| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 0.87 r_work: 0.3008 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16946 Z= 0.131 Angle : 0.615 7.305 23123 Z= 0.317 Chirality : 0.046 0.163 2334 Planarity : 0.005 0.050 3067 Dihedral : 8.506 101.962 2281 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.52 % Allowed : 12.90 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: 0.40 (0.18), residues: 1998 helix: 0.77 (0.20), residues: 718 sheet: 1.02 (0.32), residues: 294 loop : -0.27 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 382 TYR 0.026 0.002 TYR C 236 PHE 0.018 0.002 PHE A 136 TRP 0.010 0.001 TRP A 183 HIS 0.007 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00288 (16942) covalent geometry : angle 0.61506 (23123) hydrogen bonds : bond 0.05108 ( 663) hydrogen bonds : angle 6.03649 ( 1847) Misc. bond : bond 0.02126 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.694 Fit side-chains REVERT: A 203 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.6581 (mtm180) REVERT: A 315 LYS cc_start: 0.8825 (ptmm) cc_final: 0.8501 (pttm) REVERT: A 499 LYS cc_start: 0.7813 (mtpp) cc_final: 0.7516 (mtpm) REVERT: C 453 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7205 (mm-30) REVERT: C 468 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8600 (pttm) REVERT: D 237 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.7992 (mmtm) REVERT: D 315 LYS cc_start: 0.8410 (tppt) cc_final: 0.8072 (tptp) outliers start: 24 outliers final: 19 residues processed: 189 average time/residue: 0.7305 time to fit residues: 152.6965 Evaluate side-chains 188 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 468 LYS Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 237 LYS Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 361 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 15 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 110 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 158 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN B 287 ASN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN C 501 ASN D 449 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.117876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.103012 restraints weight = 35885.321| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.10 r_work: 0.2981 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16946 Z= 0.126 Angle : 0.608 7.032 23123 Z= 0.314 Chirality : 0.046 0.161 2334 Planarity : 0.005 0.049 3067 Dihedral : 8.482 101.243 2281 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.87 % Allowed : 12.67 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: 0.43 (0.18), residues: 1998 helix: 0.79 (0.20), residues: 718 sheet: 1.02 (0.32), residues: 294 loop : -0.25 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 382 TYR 0.023 0.002 TYR A 236 PHE 0.017 0.002 PHE C 136 TRP 0.010 0.001 TRP B 183 HIS 0.006 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00277 (16942) covalent geometry : angle 0.60793 (23123) hydrogen bonds : bond 0.05048 ( 663) hydrogen bonds : angle 6.00381 ( 1847) Misc. bond : bond 0.01774 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 0.631 Fit side-chains REVERT: A 203 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.6624 (mtm180) REVERT: A 315 LYS cc_start: 0.8863 (ptmm) cc_final: 0.8533 (pttm) REVERT: C 468 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8620 (pttm) REVERT: D 237 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8001 (mmtm) outliers start: 30 outliers final: 21 residues processed: 192 average time/residue: 0.6720 time to fit residues: 143.1083 Evaluate side-chains 190 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 468 LYS Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 237 LYS Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 361 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 75 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 126 optimal weight: 0.0020 chunk 120 optimal weight: 0.7980 chunk 159 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN B 287 ASN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN C 501 ASN D 449 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.119266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.104645 restraints weight = 34030.076| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.08 r_work: 0.3005 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16946 Z= 0.116 Angle : 0.587 6.706 23123 Z= 0.302 Chirality : 0.045 0.160 2334 Planarity : 0.005 0.049 3067 Dihedral : 8.307 99.273 2281 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.87 % Allowed : 12.26 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: 0.54 (0.19), residues: 1998 helix: 0.96 (0.20), residues: 704 sheet: 1.08 (0.32), residues: 294 loop : -0.23 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 382 TYR 0.023 0.002 TYR C 236 PHE 0.015 0.002 PHE A 136 TRP 0.010 0.001 TRP A 183 HIS 0.005 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00257 (16942) covalent geometry : angle 0.58682 (23123) hydrogen bonds : bond 0.04697 ( 663) hydrogen bonds : angle 5.89914 ( 1847) Misc. bond : bond 0.01707 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 0.721 Fit side-chains REVERT: A 203 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.6621 (mtm180) REVERT: A 315 LYS cc_start: 0.8827 (ptmm) cc_final: 0.8499 (pttm) REVERT: A 499 LYS cc_start: 0.7784 (mtpp) cc_final: 0.7550 (mtpm) REVERT: C 453 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7194 (mm-30) REVERT: C 476 LYS cc_start: 0.8347 (mmpt) cc_final: 0.7779 (mttt) REVERT: D 237 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8049 (mmtm) REVERT: D 315 LYS cc_start: 0.8457 (tppt) cc_final: 0.7879 (tttm) outliers start: 30 outliers final: 24 residues processed: 192 average time/residue: 0.7523 time to fit residues: 159.8512 Evaluate side-chains 191 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 237 LYS Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 361 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 93 optimal weight: 4.9990 chunk 19 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 71 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 chunk 46 optimal weight: 0.2980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN B 287 ASN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN D 449 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.116863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.102504 restraints weight = 30814.725| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.01 r_work: 0.2979 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16946 Z= 0.144 Angle : 0.640 8.679 23123 Z= 0.331 Chirality : 0.047 0.163 2334 Planarity : 0.005 0.051 3067 Dihedral : 8.615 102.320 2281 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.69 % Allowed : 12.55 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: 0.37 (0.18), residues: 1998 helix: 0.76 (0.20), residues: 718 sheet: 0.94 (0.32), residues: 294 loop : -0.27 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 382 TYR 0.028 0.002 TYR C 236 PHE 0.016 0.002 PHE A 136 TRP 0.010 0.002 TRP C 183 HIS 0.007 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00316 (16942) covalent geometry : angle 0.63965 (23123) hydrogen bonds : bond 0.05490 ( 663) hydrogen bonds : angle 6.09577 ( 1847) Misc. bond : bond 0.02211 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 0.708 Fit side-chains REVERT: A 203 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.6638 (mtm180) REVERT: A 315 LYS cc_start: 0.8863 (ptmm) cc_final: 0.8534 (pttm) REVERT: A 499 LYS cc_start: 0.7830 (mtpp) cc_final: 0.7602 (mtpm) REVERT: C 453 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7227 (mm-30) REVERT: C 476 LYS cc_start: 0.8385 (mmpt) cc_final: 0.7796 (mttt) REVERT: D 124 ASP cc_start: 0.8850 (m-30) cc_final: 0.8632 (m-30) REVERT: D 237 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.7893 (mmtm) REVERT: D 315 LYS cc_start: 0.8505 (tppt) cc_final: 0.8230 (tppt) outliers start: 27 outliers final: 24 residues processed: 191 average time/residue: 0.7219 time to fit residues: 153.1065 Evaluate side-chains 193 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 422 SER Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain D residue 12 MET Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 237 LYS Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 361 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 89 optimal weight: 2.9990 chunk 135 optimal weight: 0.3980 chunk 14 optimal weight: 0.0980 chunk 145 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 69 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 139 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN B 287 ASN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN C 501 ASN D 449 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.119717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.105669 restraints weight = 29653.249| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 0.98 r_work: 0.3022 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16946 Z= 0.112 Angle : 0.578 6.645 23123 Z= 0.297 Chirality : 0.045 0.160 2334 Planarity : 0.005 0.049 3067 Dihedral : 8.240 99.046 2281 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.69 % Allowed : 12.73 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 aren not related in a simple way. whole: 0.55 (0.19), residues: 1998 helix: 0.97 (0.20), residues: 702 sheet: 1.09 (0.32), residues: 294 loop : -0.22 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 382 TYR 0.023 0.001 TYR C 236 PHE 0.015 0.002 PHE B 136 TRP 0.010 0.001 TRP A 183 HIS 0.005 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00250 (16942) covalent geometry : angle 0.57789 (23123) hydrogen bonds : bond 0.04574 ( 663) hydrogen bonds : angle 5.86714 ( 1847) Misc. bond : bond 0.01220 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6124.99 seconds wall clock time: 105 minutes 12.58 seconds (6312.58 seconds total)