Starting phenix.real_space_refine on Mon May 19 01:51:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8el9_28225/05_2025/8el9_28225.cif Found real_map, /net/cci-nas-00/data/ceres_data/8el9_28225/05_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_28225/05_2025/8el9_28225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8el9_28225/05_2025/8el9_28225.map" model { file = "/net/cci-nas-00/data/ceres_data/8el9_28225/05_2025/8el9_28225.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8el9_28225/05_2025/8el9_28225.cif" } resolution = 2.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.113 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 17.42, per 1000 atoms: 1.00 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: 4.30 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 1.77 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: 5.30 Time building geometry restraints manager: 4.95 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 \ 501 or resid 601 through 602)) selection = (chain 'B' and (resid 5 through 18 or resid 20 through 120 or resid 122 through \ 501 or resid 601 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: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 47.780 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.090 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.012 0.002 TRP A 183 HIS 0.005 0.001 HIS A 218 PHE 0.012 0.002 PHE C 473 TYR 0.031 0.002 TYR C 236 ARG 0.009 0.000 ARG A 252 Details of bonding type rmsd hydrogen bonds : bond 0.16963 ( 663) hydrogen bonds : angle 8.01266 ( 1847) covalent geometry : bond 0.00298 (16942) covalent geometry : angle 0.65210 (23123) 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 : 1.843 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: 1.4456 time to fit residues: 318.7730 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 : 1.998 ------------------------------------------------------------------------------- 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 165 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 153 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 177 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 22 GLN D 102 HIS D 331 GLN D 372 HIS D 449 ASN D 501 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.117748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.104113 restraints weight = 26206.099| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 0.91 r_work: 0.3003 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 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 = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.0729 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= 0.134 Angle : 0.624 7.109 23123 Z= 0.324 Chirality : 0.046 0.169 2334 Planarity : 0.005 0.050 3067 Dihedral : 8.808 102.855 2298 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.34 % Allowed : 13.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.18), residues: 1998 helix: 0.69 (0.20), residues: 714 sheet: 1.02 (0.32), residues: 294 loop : -0.36 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 183 HIS 0.006 0.001 HIS A 218 PHE 0.018 0.002 PHE A 136 TYR 0.028 0.002 TYR C 236 ARG 0.005 0.001 ARG D 382 Details of bonding type rmsd hydrogen bonds : bond 0.05461 ( 663) hydrogen bonds : angle 6.32029 ( 1847) covalent geometry : bond 0.00294 (16942) covalent geometry : angle 0.62400 (23123) Misc. bond : bond 0.01849 ( 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 211 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 190 time to evaluate : 1.930 Fit side-chains REVERT: A 438 ASP cc_start: 0.8406 (t0) cc_final: 0.8184 (t0) REVERT: B 236 TYR cc_start: 0.9119 (OUTLIER) cc_final: 0.8750 (p90) REVERT: B 252 ARG cc_start: 0.8574 (ttp80) cc_final: 0.8303 (ttp80) REVERT: B 499 LYS cc_start: 0.8222 (mtpm) cc_final: 0.7807 (mtpp) REVERT: D 372 HIS cc_start: 0.7753 (m90) cc_final: 0.7550 (m170) outliers start: 21 outliers final: 11 residues processed: 203 average time/residue: 1.3906 time to fit residues: 313.3076 Evaluate side-chains 182 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 170 time to evaluate : 1.828 ------------------------------------------------------------------------------- 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 236 TYR 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 C residue 361 THR 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 35 optimal weight: 0.9980 chunk 193 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 148 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN D 22 GLN D 449 ASN D 501 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.117931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.103627 restraints weight = 31149.067| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.01 r_work: 0.2993 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16946 Z= 0.127 Angle : 0.607 7.053 23123 Z= 0.314 Chirality : 0.046 0.166 2334 Planarity : 0.005 0.050 3067 Dihedral : 8.508 101.166 2282 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.81 % Allowed : 12.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.18), residues: 1998 helix: 0.75 (0.20), residues: 718 sheet: 1.12 (0.32), residues: 294 loop : -0.29 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 183 HIS 0.006 0.001 HIS A 218 PHE 0.017 0.002 PHE A 136 TYR 0.026 0.002 TYR A 236 ARG 0.007 0.001 ARG C 252 Details of bonding type rmsd hydrogen bonds : bond 0.05154 ( 663) hydrogen bonds : angle 6.09896 ( 1847) covalent geometry : bond 0.00279 (16942) covalent geometry : angle 0.60693 (23123) Misc. bond : bond 0.01854 ( 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 206 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 1.923 Fit side-chains REVERT: A 438 ASP cc_start: 0.8445 (t0) cc_final: 0.8203 (t0) REVERT: B 236 TYR cc_start: 0.9094 (OUTLIER) cc_final: 0.8742 (p90) REVERT: B 252 ARG cc_start: 0.8567 (ttp80) cc_final: 0.8275 (ttp80) REVERT: C 124 ASP cc_start: 0.8822 (m-30) cc_final: 0.8622 (m-30) REVERT: C 453 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7218 (mm-30) REVERT: D 124 ASP cc_start: 0.8755 (m-30) cc_final: 0.8538 (m-30) outliers start: 29 outliers final: 16 residues processed: 196 average time/residue: 1.4073 time to fit residues: 307.8288 Evaluate side-chains 182 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 1.989 ------------------------------------------------------------------------------- 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 236 TYR 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 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 361 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 155 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 B 449 ASN C 235 HIS ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN D 22 GLN D 449 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.113591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.099227 restraints weight = 31282.463| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.01 r_work: 0.2933 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2835 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2835 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 16946 Z= 0.220 Angle : 0.758 8.589 23123 Z= 0.397 Chirality : 0.052 0.169 2334 Planarity : 0.006 0.052 3067 Dihedral : 9.191 106.795 2282 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.81 % Allowed : 12.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.18), residues: 1998 helix: 0.62 (0.19), residues: 714 sheet: 0.73 (0.31), residues: 294 loop : -0.56 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP D 183 HIS 0.007 0.002 HIS A 218 PHE 0.019 0.003 PHE A 136 TYR 0.030 0.003 TYR B 236 ARG 0.006 0.001 ARG D 382 Details of bonding type rmsd hydrogen bonds : bond 0.07026 ( 663) hydrogen bonds : angle 6.52040 ( 1847) covalent geometry : bond 0.00491 (16942) covalent geometry : angle 0.75844 (23123) Misc. bond : bond 0.04288 ( 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 198 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 2.192 Fit side-chains REVERT: A 203 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.6649 (mtm180) REVERT: A 236 TYR cc_start: 0.9137 (OUTLIER) cc_final: 0.8713 (p90) REVERT: B 236 TYR cc_start: 0.9165 (OUTLIER) cc_final: 0.8698 (p90) REVERT: C 236 TYR cc_start: 0.9138 (OUTLIER) cc_final: 0.8726 (p90) REVERT: D 236 TYR cc_start: 0.9133 (OUTLIER) cc_final: 0.8687 (p90) REVERT: D 237 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.7591 (mmtm) REVERT: D 394 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.6334 (mpp) outliers start: 29 outliers final: 16 residues processed: 189 average time/residue: 1.5097 time to fit residues: 316.0419 Evaluate side-chains 185 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 236 TYR 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 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 236 TYR Chi-restraints excluded: chain D residue 237 LYS Chi-restraints excluded: chain D residue 361 THR Chi-restraints excluded: chain D residue 394 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 169 optimal weight: 0.4980 chunk 165 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 154 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 185 optimal weight: 0.0980 chunk 124 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 151 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 287 ASN A 449 ASN B 287 ASN B 449 ASN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN C 501 ASN D 22 GLN D 449 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.118139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.103272 restraints weight = 35364.310| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.09 r_work: 0.2985 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 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 = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.0914 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= 0.119 Angle : 0.598 6.977 23123 Z= 0.310 Chirality : 0.045 0.163 2334 Planarity : 0.005 0.048 3067 Dihedral : 8.502 99.480 2282 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.93 % Allowed : 12.55 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.18), residues: 1998 helix: 0.78 (0.20), residues: 718 sheet: 0.96 (0.32), residues: 294 loop : -0.31 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 183 HIS 0.005 0.001 HIS A 218 PHE 0.016 0.002 PHE A 136 TYR 0.023 0.002 TYR C 236 ARG 0.006 0.001 ARG B 382 Details of bonding type rmsd hydrogen bonds : bond 0.04948 ( 663) hydrogen bonds : angle 6.02357 ( 1847) covalent geometry : bond 0.00260 (16942) covalent geometry : angle 0.59842 (23123) Misc. bond : bond 0.01192 ( 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 206 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 2.027 Fit side-chains REVERT: B 236 TYR cc_start: 0.9118 (OUTLIER) cc_final: 0.8784 (p90) REVERT: D 237 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8029 (mmtm) outliers start: 31 outliers final: 18 residues processed: 195 average time/residue: 1.3964 time to fit residues: 303.5687 Evaluate side-chains 185 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 66 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 175 optimal weight: 0.9990 chunk 184 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 287 ASN A 449 ASN B 287 ASN B 449 ASN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN D 22 GLN D 449 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.116919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.103818 restraints weight = 22971.333| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 0.84 r_work: 0.3000 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- 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 = 0.36 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: 0.8476 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16946 Z= 0.136 Angle : 0.626 7.141 23123 Z= 0.325 Chirality : 0.046 0.161 2334 Planarity : 0.005 0.048 3067 Dihedral : 8.618 100.978 2282 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.22 % Allowed : 11.85 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.18), residues: 1998 helix: 0.76 (0.20), residues: 718 sheet: 0.94 (0.32), residues: 294 loop : -0.31 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 183 HIS 0.006 0.001 HIS A 218 PHE 0.017 0.002 PHE B 136 TYR 0.024 0.002 TYR B 236 ARG 0.006 0.001 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.05341 ( 663) hydrogen bonds : angle 6.08025 ( 1847) covalent geometry : bond 0.00298 (16942) covalent geometry : angle 0.62583 (23123) Misc. bond : bond 0.01909 ( 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 207 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 170 time to evaluate : 1.911 Fit side-chains REVERT: B 236 TYR cc_start: 0.9125 (OUTLIER) cc_final: 0.8779 (p90) REVERT: D 237 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.7864 (mmtm) REVERT: D 454 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6845 (pt0) outliers start: 37 outliers final: 22 residues processed: 197 average time/residue: 1.4220 time to fit residues: 312.0838 Evaluate side-chains 190 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 236 TYR 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 146 VAL 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 12 MET Chi-restraints excluded: chain D residue 22 GLN 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 361 THR Chi-restraints excluded: chain D residue 454 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 118 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 104 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 175 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 287 ASN A 449 ASN B 53 GLN B 287 ASN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.115284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.100469 restraints weight = 35722.062| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.08 r_work: 0.2946 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 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 = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16946 Z= 0.170 Angle : 0.679 7.964 23123 Z= 0.354 Chirality : 0.049 0.164 2334 Planarity : 0.006 0.051 3067 Dihedral : 8.836 102.574 2282 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.63 % Allowed : 12.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.18), residues: 1998 helix: 0.72 (0.20), residues: 712 sheet: 0.85 (0.32), residues: 294 loop : -0.39 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 183 HIS 0.006 0.001 HIS D 63 PHE 0.017 0.003 PHE A 136 TYR 0.034 0.002 TYR C 236 ARG 0.006 0.001 ARG D 382 Details of bonding type rmsd hydrogen bonds : bond 0.05957 ( 663) hydrogen bonds : angle 6.23178 ( 1847) covalent geometry : bond 0.00376 (16942) covalent geometry : angle 0.67898 (23123) Misc. bond : bond 0.03161 ( 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 197 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 2.332 Fit side-chains REVERT: A 203 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.6596 (mtm180) REVERT: A 499 LYS cc_start: 0.7890 (mtpp) cc_final: 0.7604 (mtpm) REVERT: B 236 TYR cc_start: 0.9146 (OUTLIER) cc_final: 0.8726 (p90) REVERT: D 237 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.7754 (mmtm) REVERT: D 454 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6886 (pt0) outliers start: 26 outliers final: 19 residues processed: 188 average time/residue: 1.4902 time to fit residues: 310.3225 Evaluate side-chains 189 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 2.066 ------------------------------------------------------------------------------- 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 299 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 457 LYS Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 236 TYR 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 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 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 Chi-restraints excluded: chain D residue 454 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 128 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 141 optimal weight: 0.6980 chunk 164 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 53 GLN B 287 ASN B 449 ASN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN D 22 GLN D 449 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.118471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.104228 restraints weight = 30931.609| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.01 r_work: 0.3001 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 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 = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.0958 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 : 0.593 6.797 23123 Z= 0.307 Chirality : 0.045 0.160 2334 Planarity : 0.005 0.047 3067 Dihedral : 8.424 99.231 2282 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.98 % Allowed : 12.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.18), residues: 1998 helix: 0.80 (0.20), residues: 718 sheet: 1.01 (0.32), residues: 294 loop : -0.25 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 183 HIS 0.005 0.001 HIS A 218 PHE 0.016 0.002 PHE B 136 TYR 0.027 0.002 TYR C 236 ARG 0.007 0.000 ARG D 382 Details of bonding type rmsd hydrogen bonds : bond 0.04815 ( 663) hydrogen bonds : angle 5.94840 ( 1847) covalent geometry : bond 0.00260 (16942) covalent geometry : angle 0.59335 (23123) Misc. bond : bond 0.01210 ( 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 202 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 1.888 Fit side-chains REVERT: A 203 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.6572 (mtm180) REVERT: A 315 LYS cc_start: 0.8822 (ptmm) cc_final: 0.8500 (pttm) REVERT: B 236 TYR cc_start: 0.9084 (OUTLIER) cc_final: 0.8728 (p90) REVERT: C 453 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7216 (mm-30) REVERT: C 476 LYS cc_start: 0.8350 (mmpt) cc_final: 0.7784 (mttt) REVERT: D 237 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8047 (mmtm) REVERT: D 454 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6784 (pt0) outliers start: 32 outliers final: 23 residues processed: 192 average time/residue: 1.3751 time to fit residues: 293.4673 Evaluate side-chains 191 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 361 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 236 TYR 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 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 22 GLN 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 361 THR Chi-restraints excluded: chain D residue 454 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 136 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 170 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 53 GLN B 287 ASN B 449 ASN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN D 22 GLN D 449 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.117924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.102810 restraints weight = 38126.052| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.14 r_work: 0.2977 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 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 = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16946 Z= 0.126 Angle : 0.609 7.556 23123 Z= 0.315 Chirality : 0.046 0.161 2334 Planarity : 0.005 0.049 3067 Dihedral : 8.486 100.272 2282 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.81 % Allowed : 12.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.18), residues: 1998 helix: 0.79 (0.20), residues: 718 sheet: 1.04 (0.32), residues: 294 loop : -0.25 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 183 HIS 0.006 0.001 HIS A 218 PHE 0.017 0.002 PHE A 136 TYR 0.029 0.002 TYR C 236 ARG 0.007 0.001 ARG D 382 Details of bonding type rmsd hydrogen bonds : bond 0.05021 ( 663) hydrogen bonds : angle 5.98228 ( 1847) covalent geometry : bond 0.00279 (16942) covalent geometry : angle 0.60885 (23123) Misc. bond : bond 0.01875 ( 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 198 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 2.041 Fit side-chains REVERT: A 203 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.6594 (mtm180) REVERT: A 315 LYS cc_start: 0.8844 (ptmm) cc_final: 0.8513 (pttm) REVERT: A 499 LYS cc_start: 0.7803 (mtpp) cc_final: 0.7590 (mtpm) REVERT: B 236 TYR cc_start: 0.9096 (OUTLIER) cc_final: 0.8742 (p90) REVERT: C 453 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7248 (mm-30) REVERT: C 476 LYS cc_start: 0.8365 (mmpt) cc_final: 0.7792 (mttt) REVERT: D 237 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8002 (mmtm) REVERT: D 454 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6812 (pt0) outliers start: 29 outliers final: 21 residues processed: 190 average time/residue: 1.4676 time to fit residues: 310.1148 Evaluate side-chains 189 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 361 THR Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 236 TYR 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 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 Chi-restraints excluded: chain D residue 454 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 33 optimal weight: 0.0570 chunk 140 optimal weight: 0.5980 chunk 151 optimal weight: 0.8980 chunk 28 optimal weight: 0.2980 chunk 126 optimal weight: 0.0570 chunk 195 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 118 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- 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 53 GLN B 287 ASN B 449 ASN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN D 22 GLN D 449 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.121692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.107720 restraints weight = 29239.815| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 0.98 r_work: 0.3052 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1089 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= 0.102 Angle : 0.556 6.332 23123 Z= 0.285 Chirality : 0.044 0.158 2334 Planarity : 0.005 0.047 3067 Dihedral : 7.936 96.200 2282 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.58 % Allowed : 12.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.19), residues: 1998 helix: 1.01 (0.20), residues: 702 sheet: 1.21 (0.32), residues: 294 loop : -0.15 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 183 HIS 0.003 0.001 HIS D 218 PHE 0.013 0.001 PHE A 136 TYR 0.023 0.001 TYR C 236 ARG 0.007 0.000 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.04187 ( 663) hydrogen bonds : angle 5.74194 ( 1847) covalent geometry : bond 0.00231 (16942) covalent geometry : angle 0.55630 (23123) Misc. bond : bond 0.01106 ( 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 196 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 1.932 Fit side-chains REVERT: A 203 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.6520 (mtm180) REVERT: A 315 LYS cc_start: 0.8866 (ptmm) cc_final: 0.8534 (pttm) REVERT: A 499 LYS cc_start: 0.7682 (mtpp) cc_final: 0.7458 (mtpm) REVERT: A 501 ASN cc_start: 0.7344 (m110) cc_final: 0.7143 (m-40) REVERT: C 453 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7129 (mm-30) REVERT: C 476 LYS cc_start: 0.8342 (mmpt) cc_final: 0.7795 (mttt) REVERT: C 499 LYS cc_start: 0.8127 (mtpm) cc_final: 0.7886 (ttmm) REVERT: D 237 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8020 (mmtm) REVERT: D 499 LYS cc_start: 0.8119 (mtpm) cc_final: 0.7831 (ttmm) outliers start: 25 outliers final: 15 residues processed: 189 average time/residue: 1.6091 time to fit residues: 336.2786 Evaluate side-chains 180 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 D residue 12 MET Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 237 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 51 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 195 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 175 optimal weight: 0.0570 overall best weight: 1.5902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN B 53 GLN B 449 ASN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN D 22 GLN D 449 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.121364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.107104 restraints weight = 31386.052| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.02 r_work: 0.3042 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.190 16946 Z= 0.168 Angle : 0.791 59.155 23123 Z= 0.446 Chirality : 0.049 0.919 2334 Planarity : 0.005 0.047 3067 Dihedral : 7.811 96.262 2277 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.28 % Allowed : 12.78 % Favored : 85.93 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.19), residues: 1998 helix: 1.02 (0.20), residues: 702 sheet: 1.21 (0.32), residues: 294 loop : -0.15 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 183 HIS 0.003 0.001 HIS D 218 PHE 0.013 0.002 PHE A 136 TYR 0.023 0.002 TYR C 236 ARG 0.006 0.001 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.04286 ( 663) hydrogen bonds : angle 5.74275 ( 1847) covalent geometry : bond 0.00360 (16942) covalent geometry : angle 0.79113 (23123) Misc. bond : bond 0.01339 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12180.25 seconds wall clock time: 210 minutes 45.21 seconds (12645.21 seconds total)