Starting phenix.real_space_refine on Thu Feb 5 02:51:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dla_46868/02_2026/9dla_46868.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dla_46868/02_2026/9dla_46868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dla_46868/02_2026/9dla_46868.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dla_46868/02_2026/9dla_46868.map" model { file = "/net/cci-nas-00/data/ceres_data/9dla_46868/02_2026/9dla_46868.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dla_46868/02_2026/9dla_46868.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 40 5.16 5 C 9237 2.51 5 N 2465 2.21 5 O 2813 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14567 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3598 Classifications: {'peptide': 474} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 452} Chain: "B" Number of atoms: 3598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3598 Classifications: {'peptide': 474} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 452} Chain: "C" Number of atoms: 3581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3581 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 21, 'TRANS': 450} Chain: "D" Number of atoms: 3598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3598 Classifications: {'peptide': 474} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 452} Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.64, per 1000 atoms: 0.25 Number of scatterers: 14567 At special positions: 0 Unit cell: (103.228, 103.228, 99.288, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 12 15.00 O 2813 8.00 N 2465 7.00 C 9237 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=0, symmetry=0 Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 577.4 milliseconds 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3476 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 22 sheets defined 47.9% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 37 through 57 Proline residue: A 53 - end of helix Processing helix chain 'A' and resid 59 through 77 removed outlier: 3.818A pdb=" N TYR A 66 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 90 Processing helix chain 'A' and resid 92 through 114 Processing helix chain 'A' and resid 125 through 127 No H-bonds generated for 'chain 'A' and resid 125 through 127' Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 156 through 169 removed outlier: 4.181A pdb=" N LYS A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Proline residue: A 165 - end of helix removed outlier: 3.593A pdb=" N ALA A 169 " --> pdb=" O PRO A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 195 Processing helix chain 'A' and resid 208 through 218 removed outlier: 5.920A pdb=" N ASP A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N TYR A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 242 removed outlier: 3.845A pdb=" N GLY A 242 " --> pdb=" O GLY A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 314 through 318 Processing helix chain 'A' and resid 326 through 343 Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 389 through 399 Processing helix chain 'A' and resid 412 through 423 Processing helix chain 'A' and resid 455 through 463 Processing helix chain 'B' and resid 37 through 57 Proline residue: B 53 - end of helix Processing helix chain 'B' and resid 59 through 77 removed outlier: 3.819A pdb=" N TYR B 66 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 67 " --> pdb=" O ARG B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 90 Processing helix chain 'B' and resid 92 through 114 Processing helix chain 'B' and resid 125 through 127 No H-bonds generated for 'chain 'B' and resid 125 through 127' Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 156 through 169 removed outlier: 4.181A pdb=" N LYS B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Proline residue: B 165 - end of helix removed outlier: 3.593A pdb=" N ALA B 169 " --> pdb=" O PRO B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 195 Processing helix chain 'B' and resid 208 through 218 removed outlier: 5.920A pdb=" N ASP B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N TYR B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 242 removed outlier: 3.845A pdb=" N GLY B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 295 through 309 Processing helix chain 'B' and resid 314 through 318 Processing helix chain 'B' and resid 326 through 343 Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 389 through 399 Processing helix chain 'B' and resid 412 through 423 Processing helix chain 'B' and resid 455 through 463 Processing helix chain 'C' and resid 37 through 57 Proline residue: C 53 - end of helix Processing helix chain 'C' and resid 59 through 77 removed outlier: 3.819A pdb=" N TYR C 66 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU C 67 " --> pdb=" O ARG C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 90 Processing helix chain 'C' and resid 92 through 114 Processing helix chain 'C' and resid 125 through 127 No H-bonds generated for 'chain 'C' and resid 125 through 127' Processing helix chain 'C' and resid 128 through 132 Processing helix chain 'C' and resid 156 through 169 removed outlier: 4.181A pdb=" N LYS C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) Proline residue: C 165 - end of helix removed outlier: 3.594A pdb=" N ALA C 169 " --> pdb=" O PRO C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 195 Processing helix chain 'C' and resid 208 through 218 removed outlier: 5.921A pdb=" N ASP C 214 " --> pdb=" O SER C 210 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N TYR C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 242 removed outlier: 3.845A pdb=" N GLY C 242 " --> pdb=" O GLY C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 276 Processing helix chain 'C' and resid 295 through 309 Processing helix chain 'C' and resid 314 through 318 Processing helix chain 'C' and resid 326 through 343 Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 389 through 399 Processing helix chain 'C' and resid 412 through 423 Processing helix chain 'C' and resid 455 through 463 Processing helix chain 'D' and resid 37 through 57 Proline residue: D 53 - end of helix Processing helix chain 'D' and resid 59 through 77 removed outlier: 3.819A pdb=" N TYR D 66 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 90 Processing helix chain 'D' and resid 92 through 114 Processing helix chain 'D' and resid 125 through 127 No H-bonds generated for 'chain 'D' and resid 125 through 127' Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 156 through 169 removed outlier: 4.181A pdb=" N LYS D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) Proline residue: D 165 - end of helix removed outlier: 3.593A pdb=" N ALA D 169 " --> pdb=" O PRO D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 195 Processing helix chain 'D' and resid 208 through 218 removed outlier: 5.920A pdb=" N ASP D 214 " --> pdb=" O SER D 210 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N TYR D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 242 removed outlier: 3.845A pdb=" N GLY D 242 " --> pdb=" O GLY D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 276 Processing helix chain 'D' and resid 295 through 309 Processing helix chain 'D' and resid 314 through 318 Processing helix chain 'D' and resid 326 through 343 Processing helix chain 'D' and resid 370 through 374 Processing helix chain 'D' and resid 389 through 399 Processing helix chain 'D' and resid 412 through 423 Processing helix chain 'D' and resid 455 through 463 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 22 removed outlier: 6.173A pdb=" N ILE A 19 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N THR A 32 " --> pdb=" O ILE A 19 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE A 21 " --> pdb=" O LEU A 30 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 346 through 347 removed outlier: 6.925A pdb=" N VAL B 361 " --> pdb=" O LEU B 382 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE B 384 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE B 363 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ARG B 386 " --> pdb=" O PHE B 363 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LYS B 287 " --> pdb=" O PRO B 383 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE B 385 " --> pdb=" O LYS B 287 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL B 289 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL B 387 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL B 291 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASP B 254 " --> pdb=" O LYS B 287 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N VAL B 289 " --> pdb=" O ASP B 254 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA B 256 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N VAL B 291 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL B 258 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ALA B 255 " --> pdb=" O SER B 407 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE B 409 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU B 257 " --> pdb=" O PHE B 409 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N VAL B 428 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N SER A 468 " --> pdb=" O VAL B 428 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ILE B 430 " --> pdb=" O SER A 468 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL A 470 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ASP D 472 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ALA C 255 " --> pdb=" O SER C 407 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE C 409 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU C 257 " --> pdb=" O PHE C 409 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASP C 254 " --> pdb=" O LYS C 287 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N VAL C 289 " --> pdb=" O ASP C 254 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA C 256 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N VAL C 291 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL C 258 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LYS C 287 " --> pdb=" O PRO C 383 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE C 385 " --> pdb=" O LYS C 287 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL C 289 " --> pdb=" O ILE C 385 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL C 387 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL C 291 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL C 361 " --> pdb=" O LEU C 382 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE C 384 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE C 363 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N ARG C 386 " --> pdb=" O PHE C 363 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 202 through 204 removed outlier: 6.434A pdb=" N VAL A 146 " --> pdb=" O MET A 174 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LYS A 176 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA A 148 " --> pdb=" O LYS A 176 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE A 145 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N MET A 247 " --> pdb=" O ASN A 223 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE A 225 " --> pdb=" O MET A 247 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N GLU A 249 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N PHE A 227 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 346 through 347 removed outlier: 6.925A pdb=" N VAL A 361 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ILE A 384 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE A 363 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ARG A 386 " --> pdb=" O PHE A 363 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LYS A 287 " --> pdb=" O PRO A 383 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE A 385 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL A 289 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL A 387 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL A 291 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASP A 254 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N VAL A 289 " --> pdb=" O ASP A 254 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA A 256 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N VAL A 291 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL A 258 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ALA A 255 " --> pdb=" O SER A 407 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE A 409 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU A 257 " --> pdb=" O PHE A 409 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ASP B 472 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N VAL D 428 " --> pdb=" O VAL C 466 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N SER C 468 " --> pdb=" O VAL D 428 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE D 430 " --> pdb=" O SER C 468 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL C 470 " --> pdb=" O ILE D 430 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ALA D 255 " --> pdb=" O SER D 407 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE D 409 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU D 257 " --> pdb=" O PHE D 409 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASP D 254 " --> pdb=" O LYS D 287 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N VAL D 289 " --> pdb=" O ASP D 254 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA D 256 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N VAL D 291 " --> pdb=" O ALA D 256 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL D 258 " --> pdb=" O VAL D 291 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LYS D 287 " --> pdb=" O PRO D 383 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE D 385 " --> pdb=" O LYS D 287 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL D 289 " --> pdb=" O ILE D 385 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL D 387 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL D 291 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL D 361 " --> pdb=" O LEU D 382 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE D 384 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE D 363 " --> pdb=" O ILE D 384 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ARG D 386 " --> pdb=" O PHE D 363 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 353 through 354 removed outlier: 3.987A pdb=" N LEU A 357 " --> pdb=" O GLU A 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 443 through 444 Processing sheet with id=AA8, first strand: chain 'B' and resid 6 through 8 Processing sheet with id=AA9, first strand: chain 'B' and resid 18 through 22 removed outlier: 6.173A pdb=" N ILE B 19 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N THR B 32 " --> pdb=" O ILE B 19 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE B 21 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 202 through 204 removed outlier: 6.433A pdb=" N VAL B 146 " --> pdb=" O MET B 174 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LYS B 176 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA B 148 " --> pdb=" O LYS B 176 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE B 145 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N MET B 247 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE B 225 " --> pdb=" O MET B 247 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N GLU B 249 " --> pdb=" O ILE B 225 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE B 227 " --> pdb=" O GLU B 249 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 353 through 354 removed outlier: 3.988A pdb=" N LEU B 357 " --> pdb=" O GLU B 354 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 443 through 444 Processing sheet with id=AB4, first strand: chain 'C' and resid 6 through 8 Processing sheet with id=AB5, first strand: chain 'C' and resid 18 through 22 removed outlier: 6.172A pdb=" N ILE C 19 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N THR C 32 " --> pdb=" O ILE C 19 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE C 21 " --> pdb=" O LEU C 30 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 202 through 204 removed outlier: 6.433A pdb=" N VAL C 146 " --> pdb=" O MET C 174 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LYS C 176 " --> pdb=" O VAL C 146 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA C 148 " --> pdb=" O LYS C 176 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE C 145 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N MET C 247 " --> pdb=" O ASN C 223 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE C 225 " --> pdb=" O MET C 247 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N GLU C 249 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N PHE C 227 " --> pdb=" O GLU C 249 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 353 through 354 removed outlier: 3.988A pdb=" N LEU C 357 " --> pdb=" O GLU C 354 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 443 through 444 Processing sheet with id=AB9, first strand: chain 'D' and resid 6 through 8 Processing sheet with id=AC1, first strand: chain 'D' and resid 18 through 22 removed outlier: 6.173A pdb=" N ILE D 19 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N THR D 32 " --> pdb=" O ILE D 19 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE D 21 " --> pdb=" O LEU D 30 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 202 through 204 removed outlier: 6.434A pdb=" N VAL D 146 " --> pdb=" O MET D 174 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LYS D 176 " --> pdb=" O VAL D 146 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA D 148 " --> pdb=" O LYS D 176 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE D 145 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N MET D 247 " --> pdb=" O ASN D 223 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE D 225 " --> pdb=" O MET D 247 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N GLU D 249 " --> pdb=" O ILE D 225 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE D 227 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 353 through 354 removed outlier: 3.987A pdb=" N LEU D 357 " --> pdb=" O GLU D 354 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 443 through 444 734 hydrogen bonds defined for protein. 2067 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.06 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3960 1.33 - 1.45: 2200 1.45 - 1.57: 8571 1.57 - 1.68: 20 1.68 - 1.80: 76 Bond restraints: 14827 Sorted by residual: bond pdb=" O2B NAP D 501 " pdb=" P2B NAP D 501 " ideal model delta sigma weight residual 1.736 1.603 0.133 2.00e-02 2.50e+03 4.41e+01 bond pdb=" O2B NAP B 501 " pdb=" P2B NAP B 501 " ideal model delta sigma weight residual 1.736 1.604 0.132 2.00e-02 2.50e+03 4.38e+01 bond pdb=" O2B NAP A 501 " pdb=" P2B NAP A 501 " ideal model delta sigma weight residual 1.736 1.604 0.132 2.00e-02 2.50e+03 4.37e+01 bond pdb=" O2B NAP C 501 " pdb=" P2B NAP C 501 " ideal model delta sigma weight residual 1.736 1.604 0.132 2.00e-02 2.50e+03 4.37e+01 bond pdb=" C4A NAP B 501 " pdb=" C5A NAP B 501 " ideal model delta sigma weight residual 1.385 1.465 -0.080 2.00e-02 2.50e+03 1.60e+01 ... (remaining 14822 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 19263 1.76 - 3.51: 649 3.51 - 5.27: 161 5.27 - 7.03: 44 7.03 - 8.78: 8 Bond angle restraints: 20125 Sorted by residual: angle pdb=" CB GLU A 16 " pdb=" CG GLU A 16 " pdb=" CD GLU A 16 " ideal model delta sigma weight residual 112.60 118.39 -5.79 1.70e+00 3.46e-01 1.16e+01 angle pdb=" CB GLU B 16 " pdb=" CG GLU B 16 " pdb=" CD GLU B 16 " ideal model delta sigma weight residual 112.60 118.37 -5.77 1.70e+00 3.46e-01 1.15e+01 angle pdb=" CB GLU D 16 " pdb=" CG GLU D 16 " pdb=" CD GLU D 16 " ideal model delta sigma weight residual 112.60 118.37 -5.77 1.70e+00 3.46e-01 1.15e+01 angle pdb=" CB GLU C 16 " pdb=" CG GLU C 16 " pdb=" CD GLU C 16 " ideal model delta sigma weight residual 112.60 118.36 -5.76 1.70e+00 3.46e-01 1.15e+01 angle pdb=" CA LYS B 190 " pdb=" CB LYS B 190 " pdb=" CG LYS B 190 " ideal model delta sigma weight residual 114.10 120.64 -6.54 2.00e+00 2.50e-01 1.07e+01 ... (remaining 20120 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 8114 17.68 - 35.36: 673 35.36 - 53.04: 204 53.04 - 70.72: 124 70.72 - 88.40: 33 Dihedral angle restraints: 9148 sinusoidal: 3750 harmonic: 5398 Sorted by residual: dihedral pdb=" CA GLN B 454 " pdb=" C GLN B 454 " pdb=" N GLY B 455 " pdb=" CA GLY B 455 " ideal model delta harmonic sigma weight residual -180.00 -154.11 -25.89 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA GLN D 454 " pdb=" C GLN D 454 " pdb=" N GLY D 455 " pdb=" CA GLY D 455 " ideal model delta harmonic sigma weight residual 180.00 -154.13 -25.87 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA GLN A 454 " pdb=" C GLN A 454 " pdb=" N GLY A 455 " pdb=" CA GLY A 455 " ideal model delta harmonic sigma weight residual -180.00 -154.14 -25.86 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 9145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1675 0.048 - 0.097: 492 0.097 - 0.145: 122 0.145 - 0.194: 20 0.194 - 0.242: 12 Chirality restraints: 2321 Sorted by residual: chirality pdb=" C2B NAP D 501 " pdb=" C1B NAP D 501 " pdb=" C3B NAP D 501 " pdb=" O2B NAP D 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.51 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" C2B NAP C 501 " pdb=" C1B NAP C 501 " pdb=" C3B NAP C 501 " pdb=" O2B NAP C 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.51 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" C2B NAP B 501 " pdb=" C1B NAP B 501 " pdb=" C3B NAP B 501 " pdb=" O2B NAP B 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.51 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 2318 not shown) Planarity restraints: 2593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 378 " 0.024 2.00e-02 2.50e+03 3.75e-02 2.46e+01 pdb=" CG PHE B 378 " -0.079 2.00e-02 2.50e+03 pdb=" CD1 PHE B 378 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE B 378 " 0.047 2.00e-02 2.50e+03 pdb=" CE1 PHE B 378 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE B 378 " -0.021 2.00e-02 2.50e+03 pdb=" CZ PHE B 378 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 378 " -0.024 2.00e-02 2.50e+03 3.74e-02 2.45e+01 pdb=" CG PHE A 378 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 PHE A 378 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 378 " -0.047 2.00e-02 2.50e+03 pdb=" CE1 PHE A 378 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE A 378 " 0.021 2.00e-02 2.50e+03 pdb=" CZ PHE A 378 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 378 " 0.024 2.00e-02 2.50e+03 3.74e-02 2.45e+01 pdb=" CG PHE D 378 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 PHE D 378 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE D 378 " 0.048 2.00e-02 2.50e+03 pdb=" CE1 PHE D 378 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE D 378 " -0.021 2.00e-02 2.50e+03 pdb=" CZ PHE D 378 " 0.002 2.00e-02 2.50e+03 ... (remaining 2590 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 824 2.72 - 3.27: 14800 3.27 - 3.81: 25322 3.81 - 4.36: 33161 4.36 - 4.90: 56319 Nonbonded interactions: 130426 Sorted by model distance: nonbonded pdb=" NH2 ARG A 56 " pdb=" OE1 GLU A 141 " model vdw 2.176 3.120 nonbonded pdb=" NH2 ARG C 56 " pdb=" OE1 GLU C 141 " model vdw 2.177 3.120 nonbonded pdb=" NH2 ARG B 56 " pdb=" OE1 GLU B 141 " model vdw 2.177 3.120 nonbonded pdb=" NH2 ARG D 56 " pdb=" OE1 GLU D 141 " model vdw 2.177 3.120 nonbonded pdb=" OG SER B 230 " pdb=" O1A NAP B 501 " model vdw 2.193 3.040 ... (remaining 130421 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 1 through 472 or resid 501)) selection = (chain 'B' and (resid 1 through 472 or resid 501)) selection = chain 'C' selection = (chain 'D' and (resid 1 through 472 or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.710 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 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 : 0.008 0.133 14827 Z= 0.357 Angle : 0.825 8.785 20125 Z= 0.421 Chirality : 0.051 0.242 2321 Planarity : 0.005 0.045 2593 Dihedral : 17.369 88.400 5672 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.21 % Allowed : 2.41 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.19), residues: 1886 helix: 0.51 (0.18), residues: 828 sheet: -0.85 (0.24), residues: 407 loop : -0.40 (0.26), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 208 TYR 0.022 0.002 TYR B 4 PHE 0.079 0.004 PHE B 378 TRP 0.014 0.002 TRP D 359 HIS 0.002 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00824 (14827) covalent geometry : angle 0.82454 (20125) hydrogen bonds : bond 0.13737 ( 734) hydrogen bonds : angle 6.71830 ( 2067) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 270 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7541 (mmpt) REVERT: A 304 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7368 (pp30) REVERT: A 326 ASP cc_start: 0.7444 (p0) cc_final: 0.7086 (m-30) REVERT: A 457 LYS cc_start: 0.8059 (tptt) cc_final: 0.7812 (ttpt) REVERT: B 120 GLN cc_start: 0.7755 (mt0) cc_final: 0.7492 (mt0) REVERT: B 208 ARG cc_start: 0.7403 (mmt180) cc_final: 0.7124 (mmm160) REVERT: B 368 LYS cc_start: 0.7638 (OUTLIER) cc_final: 0.7411 (mtmm) REVERT: C 16 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6471 (tt0) REVERT: C 368 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7131 (mttm) REVERT: D 1 MET cc_start: 0.4122 (OUTLIER) cc_final: 0.3908 (tpp) REVERT: D 13 LYS cc_start: 0.8226 (mtpt) cc_final: 0.7984 (mtpp) outliers start: 48 outliers final: 2 residues processed: 283 average time/residue: 0.9069 time to fit residues: 274.2163 Evaluate side-chains 166 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 158 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 368 LYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 292 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 ASN A 157 ASN ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 GLN A 431 ASN B 6 ASN B 157 ASN B 341 GLN B 356 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN C 411 ASN D 6 ASN ** D 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.126503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.107069 restraints weight = 16419.713| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.41 r_work: 0.3088 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14827 Z= 0.130 Angle : 0.523 6.777 20125 Z= 0.270 Chirality : 0.044 0.220 2321 Planarity : 0.004 0.045 2593 Dihedral : 12.770 79.490 2295 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.34 % Allowed : 10.11 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.20), residues: 1886 helix: 1.17 (0.18), residues: 822 sheet: -0.80 (0.23), residues: 419 loop : -0.19 (0.26), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 236 TYR 0.006 0.001 TYR A 215 PHE 0.014 0.001 PHE D 413 TRP 0.009 0.001 TRP A 12 HIS 0.001 0.000 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00300 (14827) covalent geometry : angle 0.52264 (20125) hydrogen bonds : bond 0.04004 ( 734) hydrogen bonds : angle 4.95931 ( 2067) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 0.605 Fit side-chains REVERT: A 1 MET cc_start: 0.5096 (mmm) cc_final: 0.4888 (tpt) REVERT: A 94 LYS cc_start: 0.8337 (mtmt) cc_final: 0.7553 (mmtt) REVERT: A 123 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8076 (mt-10) REVERT: A 174 MET cc_start: 0.8824 (mmm) cc_final: 0.8345 (mmm) REVERT: A 263 ASP cc_start: 0.7746 (t0) cc_final: 0.7412 (t0) REVERT: A 457 LYS cc_start: 0.8469 (tptt) cc_final: 0.7882 (ttpt) REVERT: B 46 GLN cc_start: 0.8119 (mm110) cc_final: 0.7409 (mt0) REVERT: B 120 GLN cc_start: 0.8432 (mt0) cc_final: 0.8112 (mt0) REVERT: B 174 MET cc_start: 0.8548 (mmm) cc_final: 0.7965 (mmm) REVERT: B 208 ARG cc_start: 0.7389 (mmt180) cc_final: 0.6798 (mmm160) REVERT: B 235 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7585 (mm-30) REVERT: B 369 ASP cc_start: 0.7795 (m-30) cc_final: 0.7178 (t0) REVERT: C 1 MET cc_start: 0.5316 (mmm) cc_final: 0.4364 (mpp) REVERT: C 11 LYS cc_start: 0.7838 (pmtt) cc_final: 0.7366 (pptt) REVERT: C 239 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.6826 (mtm110) REVERT: C 368 LYS cc_start: 0.7973 (mtmt) cc_final: 0.7337 (mttm) REVERT: C 369 ASP cc_start: 0.7827 (m-30) cc_final: 0.7542 (m-30) REVERT: C 461 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7540 (pt0) REVERT: D 1 MET cc_start: 0.4734 (tpp) cc_final: 0.4456 (ttm) REVERT: D 13 LYS cc_start: 0.8163 (mtpt) cc_final: 0.7847 (mtpp) REVERT: D 352 LYS cc_start: 0.7446 (ttpt) cc_final: 0.7075 (tttt) outliers start: 20 outliers final: 5 residues processed: 200 average time/residue: 0.9063 time to fit residues: 193.9561 Evaluate side-chains 157 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 151 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain C residue 239 ARG Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 197 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 107 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 chunk 180 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN D 120 GLN D 157 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.116170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.094444 restraints weight = 16654.985| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.71 r_work: 0.2924 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 14827 Z= 0.222 Angle : 0.580 6.361 20125 Z= 0.298 Chirality : 0.045 0.239 2321 Planarity : 0.004 0.033 2593 Dihedral : 11.857 80.636 2269 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.01 % Allowed : 11.58 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.20), residues: 1886 helix: 1.10 (0.18), residues: 822 sheet: -0.81 (0.24), residues: 397 loop : -0.22 (0.26), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 236 TYR 0.024 0.002 TYR C 4 PHE 0.020 0.002 PHE A 413 TRP 0.009 0.002 TRP C 359 HIS 0.003 0.001 HIS D 266 Details of bonding type rmsd covalent geometry : bond 0.00541 (14827) covalent geometry : angle 0.58048 (20125) hydrogen bonds : bond 0.04431 ( 734) hydrogen bonds : angle 4.88271 ( 2067) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 0.579 Fit side-chains REVERT: A 16 GLU cc_start: 0.7911 (tp30) cc_final: 0.7611 (mm-30) REVERT: A 123 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8307 (mt-10) REVERT: A 174 MET cc_start: 0.8922 (mmm) cc_final: 0.8433 (mmm) REVERT: A 243 MET cc_start: 0.8582 (ttm) cc_final: 0.8318 (ttp) REVERT: A 261 ASP cc_start: 0.8577 (p0) cc_final: 0.8277 (p0) REVERT: A 317 ASP cc_start: 0.7216 (m-30) cc_final: 0.6936 (m-30) REVERT: A 391 GLU cc_start: 0.8215 (mp0) cc_final: 0.7784 (mp0) REVERT: A 457 LYS cc_start: 0.8445 (tptt) cc_final: 0.7761 (ttpt) REVERT: B 11 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.7442 (pttm) REVERT: B 18 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7146 (mt-10) REVERT: B 46 GLN cc_start: 0.8311 (mm110) cc_final: 0.7786 (mt0) REVERT: B 120 GLN cc_start: 0.8651 (mt0) cc_final: 0.8324 (mt0) REVERT: B 174 MET cc_start: 0.8627 (mmm) cc_final: 0.8041 (mmm) REVERT: B 211 GLU cc_start: 0.7708 (pt0) cc_final: 0.7389 (mt-10) REVERT: B 368 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7728 (ptmm) REVERT: B 401 GLU cc_start: 0.7595 (mp0) cc_final: 0.7021 (pt0) REVERT: B 421 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7767 (pt0) REVERT: C 1 MET cc_start: 0.5608 (OUTLIER) cc_final: 0.4477 (mpp) REVERT: C 11 LYS cc_start: 0.7901 (pmtt) cc_final: 0.7331 (ptpt) REVERT: C 214 ASP cc_start: 0.8713 (m-30) cc_final: 0.8316 (m-30) REVERT: C 235 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7174 (mm-30) REVERT: C 239 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.6821 (mtm110) REVERT: C 368 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7311 (mttm) REVERT: D 1 MET cc_start: 0.5091 (tpp) cc_final: 0.4653 (ttp) REVERT: D 11 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7358 (ptpt) REVERT: D 13 LYS cc_start: 0.8197 (mtpt) cc_final: 0.7686 (mtpp) REVERT: D 75 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7847 (mm-30) REVERT: D 214 ASP cc_start: 0.8439 (m-30) cc_final: 0.7657 (p0) REVERT: D 263 ASP cc_start: 0.8255 (t0) cc_final: 0.7891 (t70) REVERT: D 352 LYS cc_start: 0.7604 (tttt) cc_final: 0.7209 (tttt) REVERT: D 421 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7842 (mt-10) outliers start: 30 outliers final: 10 residues processed: 183 average time/residue: 0.9145 time to fit residues: 178.9135 Evaluate side-chains 169 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 239 ARG Chi-restraints excluded: chain C residue 368 LYS Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 11 LYS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 368 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 185 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 129 optimal weight: 0.1980 chunk 120 optimal weight: 9.9990 chunk 99 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 ASN D 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.120829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.099796 restraints weight = 16514.780| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.63 r_work: 0.3006 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14827 Z= 0.123 Angle : 0.483 5.142 20125 Z= 0.248 Chirality : 0.043 0.230 2321 Planarity : 0.004 0.032 2593 Dihedral : 11.117 81.903 2269 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.01 % Allowed : 12.52 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.20), residues: 1886 helix: 1.41 (0.18), residues: 822 sheet: -0.68 (0.25), residues: 386 loop : -0.05 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 236 TYR 0.016 0.001 TYR C 4 PHE 0.013 0.001 PHE A 413 TRP 0.009 0.001 TRP A 12 HIS 0.001 0.000 HIS D 266 Details of bonding type rmsd covalent geometry : bond 0.00285 (14827) covalent geometry : angle 0.48296 (20125) hydrogen bonds : bond 0.03667 ( 734) hydrogen bonds : angle 4.55628 ( 2067) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.586 Fit side-chains REVERT: A 16 GLU cc_start: 0.7905 (tp30) cc_final: 0.7630 (mm-30) REVERT: A 123 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8215 (mt-10) REVERT: A 141 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7788 (pt0) REVERT: A 174 MET cc_start: 0.8851 (mmm) cc_final: 0.8433 (mmm) REVERT: A 261 ASP cc_start: 0.8527 (p0) cc_final: 0.8303 (p0) REVERT: A 317 ASP cc_start: 0.7199 (m-30) cc_final: 0.6920 (m-30) REVERT: A 326 ASP cc_start: 0.7331 (p0) cc_final: 0.7115 (p0) REVERT: A 369 ASP cc_start: 0.8159 (m-30) cc_final: 0.7736 (m-30) REVERT: A 391 GLU cc_start: 0.8153 (mp0) cc_final: 0.7797 (mp0) REVERT: A 457 LYS cc_start: 0.8475 (tptt) cc_final: 0.7821 (ttpt) REVERT: B 13 LYS cc_start: 0.8442 (mtpm) cc_final: 0.7399 (mttt) REVERT: B 46 GLN cc_start: 0.8283 (mm110) cc_final: 0.7886 (mt0) REVERT: B 120 GLN cc_start: 0.8585 (mt0) cc_final: 0.8039 (mp10) REVERT: B 174 MET cc_start: 0.8564 (mmm) cc_final: 0.8068 (mmm) REVERT: B 208 ARG cc_start: 0.7351 (mpt90) cc_final: 0.6656 (mmm160) REVERT: B 235 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7562 (mm-30) REVERT: B 368 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7753 (ptmm) REVERT: B 401 GLU cc_start: 0.7363 (mp0) cc_final: 0.6862 (pt0) REVERT: B 421 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7769 (pt0) REVERT: C 11 LYS cc_start: 0.7807 (pmtt) cc_final: 0.7383 (ptpt) REVERT: C 122 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8721 (mtm) REVERT: C 214 ASP cc_start: 0.8695 (m-30) cc_final: 0.8337 (m-30) REVERT: C 220 LYS cc_start: 0.8131 (mppt) cc_final: 0.7494 (mppt) REVERT: C 235 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7321 (mm-30) REVERT: C 239 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.6883 (mtm110) REVERT: D 1 MET cc_start: 0.5217 (tpp) cc_final: 0.4871 (ttp) REVERT: D 11 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.7327 (ptpt) REVERT: D 13 LYS cc_start: 0.8129 (mtpt) cc_final: 0.7756 (mtpp) REVERT: D 75 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7792 (mm-30) REVERT: D 214 ASP cc_start: 0.8270 (m-30) cc_final: 0.7555 (p0) REVERT: D 220 LYS cc_start: 0.8400 (mppt) cc_final: 0.7970 (mmtm) REVERT: D 263 ASP cc_start: 0.8217 (t0) cc_final: 0.7893 (t70) REVERT: D 352 LYS cc_start: 0.7718 (tttt) cc_final: 0.7392 (tttt) REVERT: D 421 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7908 (mt-10) outliers start: 30 outliers final: 10 residues processed: 196 average time/residue: 0.8905 time to fit residues: 186.9547 Evaluate side-chains 179 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 239 ARG Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 11 LYS Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 210 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 155 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 chunk 109 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.117266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.095695 restraints weight = 16498.129| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.69 r_work: 0.2958 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14827 Z= 0.182 Angle : 0.532 7.393 20125 Z= 0.271 Chirality : 0.044 0.238 2321 Planarity : 0.004 0.033 2593 Dihedral : 11.134 82.645 2269 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.48 % Allowed : 12.92 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.20), residues: 1886 helix: 1.36 (0.18), residues: 822 sheet: -0.54 (0.26), residues: 365 loop : -0.04 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 236 TYR 0.022 0.001 TYR C 4 PHE 0.016 0.002 PHE A 413 TRP 0.009 0.001 TRP A 12 HIS 0.002 0.001 HIS D 266 Details of bonding type rmsd covalent geometry : bond 0.00439 (14827) covalent geometry : angle 0.53192 (20125) hydrogen bonds : bond 0.03984 ( 734) hydrogen bonds : angle 4.60523 ( 2067) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 0.573 Fit side-chains REVERT: A 16 GLU cc_start: 0.7957 (tp30) cc_final: 0.7631 (mm-30) REVERT: A 36 MET cc_start: 0.8904 (mtp) cc_final: 0.8584 (mtp) REVERT: A 123 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8323 (mt-10) REVERT: A 174 MET cc_start: 0.8912 (mmm) cc_final: 0.8440 (mmm) REVERT: A 261 ASP cc_start: 0.8582 (p0) cc_final: 0.8278 (p0) REVERT: A 317 ASP cc_start: 0.7209 (m-30) cc_final: 0.6910 (m-30) REVERT: A 326 ASP cc_start: 0.7293 (p0) cc_final: 0.7089 (p0) REVERT: A 391 GLU cc_start: 0.8154 (mp0) cc_final: 0.7758 (mp0) REVERT: A 421 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7594 (tm-30) REVERT: A 457 LYS cc_start: 0.8432 (tptt) cc_final: 0.7727 (ttpt) REVERT: B 13 LYS cc_start: 0.8404 (mtpm) cc_final: 0.7333 (mttt) REVERT: B 46 GLN cc_start: 0.8177 (mm110) cc_final: 0.7794 (mt0) REVERT: B 120 GLN cc_start: 0.8614 (mt0) cc_final: 0.8025 (mp10) REVERT: B 174 MET cc_start: 0.8608 (mmm) cc_final: 0.8043 (mmm) REVERT: B 208 ARG cc_start: 0.7342 (mpt90) cc_final: 0.6966 (tpp-160) REVERT: B 368 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7773 (ptmm) REVERT: B 401 GLU cc_start: 0.7447 (mp0) cc_final: 0.6845 (pt0) REVERT: B 421 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7677 (pt0) REVERT: C 11 LYS cc_start: 0.7717 (pmtt) cc_final: 0.7257 (ptpt) REVERT: C 17 GLN cc_start: 0.7211 (mp10) cc_final: 0.6497 (mp-120) REVERT: C 214 ASP cc_start: 0.8638 (m-30) cc_final: 0.8235 (m-30) REVERT: C 220 LYS cc_start: 0.8140 (mppt) cc_final: 0.7537 (mppt) REVERT: C 235 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7166 (mm-30) REVERT: C 239 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.6766 (mtm110) REVERT: C 368 LYS cc_start: 0.7849 (mtmm) cc_final: 0.7441 (ptpt) REVERT: D 1 MET cc_start: 0.5334 (tpp) cc_final: 0.4923 (ttp) REVERT: D 11 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.7225 (ptpt) REVERT: D 13 LYS cc_start: 0.8103 (mtpt) cc_final: 0.7682 (mtpp) REVERT: D 75 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7848 (mm-30) REVERT: D 214 ASP cc_start: 0.8253 (m-30) cc_final: 0.7418 (p0) REVERT: D 220 LYS cc_start: 0.8277 (mppt) cc_final: 0.7819 (mmtm) REVERT: D 263 ASP cc_start: 0.8267 (t0) cc_final: 0.7886 (t70) REVERT: D 269 LYS cc_start: 0.8012 (mttt) cc_final: 0.7614 (mtmm) REVERT: D 352 LYS cc_start: 0.7647 (tttt) cc_final: 0.7268 (tttt) REVERT: D 368 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.8095 (pttt) outliers start: 37 outliers final: 13 residues processed: 185 average time/residue: 0.8835 time to fit residues: 175.2010 Evaluate side-chains 174 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 239 ARG Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 11 LYS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 368 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 21 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 180 optimal weight: 6.9990 chunk 116 optimal weight: 0.6980 chunk 142 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.116439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.094924 restraints weight = 16463.988| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.69 r_work: 0.2956 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 14827 Z= 0.215 Angle : 0.553 6.815 20125 Z= 0.282 Chirality : 0.045 0.248 2321 Planarity : 0.004 0.033 2593 Dihedral : 11.147 83.087 2269 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.28 % Allowed : 13.45 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.20), residues: 1886 helix: 1.23 (0.18), residues: 824 sheet: -0.58 (0.26), residues: 365 loop : -0.11 (0.25), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 236 TYR 0.023 0.002 TYR C 4 PHE 0.019 0.002 PHE C 378 TRP 0.010 0.002 TRP A 12 HIS 0.002 0.001 HIS D 266 Details of bonding type rmsd covalent geometry : bond 0.00524 (14827) covalent geometry : angle 0.55330 (20125) hydrogen bonds : bond 0.04180 ( 734) hydrogen bonds : angle 4.66314 ( 2067) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 0.660 Fit side-chains REVERT: A 16 GLU cc_start: 0.7985 (tp30) cc_final: 0.7663 (mm-30) REVERT: A 123 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8343 (mt-10) REVERT: A 174 MET cc_start: 0.8931 (mmm) cc_final: 0.8457 (mmm) REVERT: A 247 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8415 (mtt) REVERT: A 317 ASP cc_start: 0.7259 (m-30) cc_final: 0.6938 (m-30) REVERT: A 391 GLU cc_start: 0.8128 (mp0) cc_final: 0.7824 (mp0) REVERT: A 421 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7611 (tm-30) REVERT: A 457 LYS cc_start: 0.8465 (tptt) cc_final: 0.7753 (ttpt) REVERT: B 13 LYS cc_start: 0.8430 (mtpm) cc_final: 0.7348 (mttt) REVERT: B 46 GLN cc_start: 0.8179 (mm110) cc_final: 0.7859 (mt0) REVERT: B 120 GLN cc_start: 0.8610 (mt0) cc_final: 0.8035 (mt0) REVERT: B 208 ARG cc_start: 0.7442 (mpt90) cc_final: 0.7066 (tpp-160) REVERT: B 211 GLU cc_start: 0.7661 (pt0) cc_final: 0.7422 (mt-10) REVERT: B 235 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7639 (mt-10) REVERT: B 331 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7834 (m-30) REVERT: B 368 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7864 (ptmm) REVERT: B 401 GLU cc_start: 0.7528 (mp0) cc_final: 0.6938 (pt0) REVERT: B 421 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7642 (pt0) REVERT: C 1 MET cc_start: 0.5586 (OUTLIER) cc_final: 0.4551 (mpp) REVERT: C 11 LYS cc_start: 0.7746 (pmtt) cc_final: 0.7252 (ptpt) REVERT: C 17 GLN cc_start: 0.7213 (mp10) cc_final: 0.6547 (mp-120) REVERT: C 122 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8801 (mtm) REVERT: C 214 ASP cc_start: 0.8643 (m-30) cc_final: 0.8348 (m-30) REVERT: C 220 LYS cc_start: 0.8157 (mppt) cc_final: 0.7591 (mppt) REVERT: C 235 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7192 (mm-30) REVERT: C 239 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6750 (mtm110) REVERT: C 368 LYS cc_start: 0.7992 (mtmm) cc_final: 0.7602 (ptpp) REVERT: D 1 MET cc_start: 0.5751 (tpp) cc_final: 0.5324 (ttp) REVERT: D 11 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.7265 (ptpt) REVERT: D 13 LYS cc_start: 0.8080 (mtpt) cc_final: 0.7547 (mtpp) REVERT: D 75 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7866 (mm-30) REVERT: D 214 ASP cc_start: 0.8246 (m-30) cc_final: 0.7484 (p0) REVERT: D 220 LYS cc_start: 0.8266 (mppt) cc_final: 0.7828 (mmtm) REVERT: D 243 MET cc_start: 0.8994 (mtp) cc_final: 0.8719 (ttm) REVERT: D 263 ASP cc_start: 0.8313 (t0) cc_final: 0.7903 (t70) REVERT: D 269 LYS cc_start: 0.8054 (mttt) cc_final: 0.7651 (mtmm) REVERT: D 305 GLU cc_start: 0.6661 (pt0) cc_final: 0.6439 (pt0) REVERT: D 352 LYS cc_start: 0.7754 (tttt) cc_final: 0.7537 (tttt) REVERT: D 368 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.8104 (pttt) REVERT: D 421 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7672 (mm-30) outliers start: 34 outliers final: 14 residues processed: 180 average time/residue: 0.8791 time to fit residues: 169.8119 Evaluate side-chains 181 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 239 ARG Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 11 LYS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 368 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 50 optimal weight: 0.9990 chunk 179 optimal weight: 4.9990 chunk 182 optimal weight: 0.7980 chunk 166 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN A 431 ASN A 454 GLN D 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.122218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.102147 restraints weight = 16310.594| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.49 r_work: 0.3023 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14827 Z= 0.116 Angle : 0.471 5.797 20125 Z= 0.240 Chirality : 0.042 0.222 2321 Planarity : 0.004 0.033 2593 Dihedral : 10.480 83.757 2269 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.01 % Allowed : 14.19 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.20), residues: 1886 helix: 1.50 (0.18), residues: 825 sheet: -0.44 (0.26), residues: 365 loop : 0.03 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 236 TYR 0.014 0.001 TYR C 4 PHE 0.011 0.001 PHE A 378 TRP 0.010 0.001 TRP A 12 HIS 0.001 0.000 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00268 (14827) covalent geometry : angle 0.47062 (20125) hydrogen bonds : bond 0.03552 ( 734) hydrogen bonds : angle 4.43089 ( 2067) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7933 (tp30) cc_final: 0.7647 (mm-30) REVERT: A 123 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8185 (mt-10) REVERT: A 174 MET cc_start: 0.8821 (mmm) cc_final: 0.8429 (mmm) REVERT: A 247 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8289 (mtt) REVERT: A 261 ASP cc_start: 0.8545 (p0) cc_final: 0.8322 (p0) REVERT: A 317 ASP cc_start: 0.7327 (m-30) cc_final: 0.7007 (m-30) REVERT: A 369 ASP cc_start: 0.8133 (m-30) cc_final: 0.7710 (m-30) REVERT: A 391 GLU cc_start: 0.8107 (mp0) cc_final: 0.7779 (mp0) REVERT: A 421 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7651 (tm-30) REVERT: A 457 LYS cc_start: 0.8483 (tptt) cc_final: 0.7865 (ttpt) REVERT: B 13 LYS cc_start: 0.8433 (mtpm) cc_final: 0.7393 (mttt) REVERT: B 46 GLN cc_start: 0.8204 (mm110) cc_final: 0.7997 (mt0) REVERT: B 120 GLN cc_start: 0.8523 (mt0) cc_final: 0.8025 (mp10) REVERT: B 174 MET cc_start: 0.8607 (mmm) cc_final: 0.7940 (mmm) REVERT: B 208 ARG cc_start: 0.7339 (mpt90) cc_final: 0.6993 (tpp-160) REVERT: B 235 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7582 (mm-30) REVERT: B 331 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7909 (m-30) REVERT: B 368 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7861 (ptmm) REVERT: B 401 GLU cc_start: 0.7338 (mp0) cc_final: 0.6876 (pt0) REVERT: C 11 LYS cc_start: 0.7729 (pmtt) cc_final: 0.7393 (ptpt) REVERT: C 17 GLN cc_start: 0.7288 (mp10) cc_final: 0.6662 (mp-120) REVERT: C 122 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8686 (mtm) REVERT: C 214 ASP cc_start: 0.8657 (m-30) cc_final: 0.8439 (m-30) REVERT: C 220 LYS cc_start: 0.8198 (mppt) cc_final: 0.7659 (mppt) REVERT: C 235 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7272 (mm-30) REVERT: C 239 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6777 (mtm110) REVERT: C 368 LYS cc_start: 0.7950 (mtmm) cc_final: 0.7567 (ptpp) REVERT: C 461 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7549 (pt0) REVERT: D 1 MET cc_start: 0.5850 (tpp) cc_final: 0.5412 (ttp) REVERT: D 11 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7338 (ptpt) REVERT: D 75 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7767 (mm-30) REVERT: D 214 ASP cc_start: 0.8061 (m-30) cc_final: 0.7414 (p0) REVERT: D 220 LYS cc_start: 0.8300 (mppt) cc_final: 0.7948 (mmtm) REVERT: D 243 MET cc_start: 0.8978 (mtp) cc_final: 0.8710 (ttm) REVERT: D 263 ASP cc_start: 0.8342 (t0) cc_final: 0.7987 (t70) REVERT: D 269 LYS cc_start: 0.7964 (mttt) cc_final: 0.7589 (mtmm) REVERT: D 305 GLU cc_start: 0.6748 (pt0) cc_final: 0.6535 (pt0) REVERT: D 352 LYS cc_start: 0.7883 (tttt) cc_final: 0.7586 (tttt) REVERT: D 421 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7712 (mm-30) outliers start: 30 outliers final: 12 residues processed: 198 average time/residue: 0.8597 time to fit residues: 182.7932 Evaluate side-chains 182 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 239 ARG Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 11 LYS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 210 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 7.9990 chunk 36 optimal weight: 0.4980 chunk 3 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 31 optimal weight: 0.0970 chunk 179 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.119153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.098238 restraints weight = 16522.895| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.61 r_work: 0.2975 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14827 Z= 0.151 Angle : 0.500 5.756 20125 Z= 0.255 Chirality : 0.043 0.240 2321 Planarity : 0.004 0.032 2593 Dihedral : 10.628 84.659 2269 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.94 % Allowed : 14.66 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.20), residues: 1886 helix: 1.47 (0.18), residues: 825 sheet: -0.35 (0.26), residues: 395 loop : 0.06 (0.26), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 236 TYR 0.018 0.001 TYR C 4 PHE 0.012 0.001 PHE A 378 TRP 0.009 0.001 TRP A 12 HIS 0.003 0.001 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00358 (14827) covalent geometry : angle 0.50035 (20125) hydrogen bonds : bond 0.03758 ( 734) hydrogen bonds : angle 4.45013 ( 2067) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7947 (tp30) cc_final: 0.7654 (mm-30) REVERT: A 36 MET cc_start: 0.8823 (mtp) cc_final: 0.8578 (mtp) REVERT: A 123 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8242 (mt-10) REVERT: A 174 MET cc_start: 0.8864 (mmm) cc_final: 0.8428 (mmm) REVERT: A 211 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6661 (mt-10) REVERT: A 247 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8343 (mtt) REVERT: A 317 ASP cc_start: 0.7337 (m-30) cc_final: 0.7027 (m-30) REVERT: A 369 ASP cc_start: 0.8201 (m-30) cc_final: 0.7775 (m-30) REVERT: A 391 GLU cc_start: 0.8129 (mp0) cc_final: 0.7798 (mp0) REVERT: A 421 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7670 (tm-30) REVERT: A 457 LYS cc_start: 0.8473 (tptt) cc_final: 0.7841 (ttpt) REVERT: B 13 LYS cc_start: 0.8403 (mtpm) cc_final: 0.7351 (mttt) REVERT: B 46 GLN cc_start: 0.8242 (mm110) cc_final: 0.8021 (mt0) REVERT: B 120 GLN cc_start: 0.8592 (mt0) cc_final: 0.8059 (mp10) REVERT: B 174 MET cc_start: 0.8633 (mmm) cc_final: 0.7989 (mmm) REVERT: B 208 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.7032 (tpp-160) REVERT: B 235 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7466 (mm-30) REVERT: B 261 ASP cc_start: 0.8533 (p0) cc_final: 0.8327 (p0) REVERT: B 331 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7929 (m-30) REVERT: B 368 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7858 (ptmm) REVERT: B 401 GLU cc_start: 0.7450 (mp0) cc_final: 0.6977 (pt0) REVERT: B 421 GLU cc_start: 0.8154 (pp20) cc_final: 0.7676 (mt-10) REVERT: C 11 LYS cc_start: 0.7748 (pmtt) cc_final: 0.7365 (ptpt) REVERT: C 17 GLN cc_start: 0.7330 (mp10) cc_final: 0.6629 (mp-120) REVERT: C 122 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8725 (mtm) REVERT: C 214 ASP cc_start: 0.8684 (m-30) cc_final: 0.8462 (m-30) REVERT: C 220 LYS cc_start: 0.8189 (mppt) cc_final: 0.7653 (mppt) REVERT: C 235 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7355 (mm-30) REVERT: C 239 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6733 (mtm110) REVERT: C 368 LYS cc_start: 0.7967 (mtmm) cc_final: 0.7584 (ptpp) REVERT: C 461 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7541 (tt0) REVERT: D 1 MET cc_start: 0.5898 (tpp) cc_final: 0.5446 (ttp) REVERT: D 11 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7357 (ptpt) REVERT: D 75 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7823 (mm-30) REVERT: D 214 ASP cc_start: 0.7902 (m-30) cc_final: 0.7387 (p0) REVERT: D 220 LYS cc_start: 0.8347 (mppt) cc_final: 0.7950 (mmtm) REVERT: D 263 ASP cc_start: 0.8345 (t0) cc_final: 0.7975 (t70) REVERT: D 269 LYS cc_start: 0.8074 (mttt) cc_final: 0.7710 (mtmm) REVERT: D 305 GLU cc_start: 0.6800 (pt0) cc_final: 0.6584 (pt0) REVERT: D 352 LYS cc_start: 0.7848 (tttt) cc_final: 0.7640 (tttt) REVERT: D 421 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7674 (mm-30) outliers start: 29 outliers final: 14 residues processed: 179 average time/residue: 0.8766 time to fit residues: 168.4441 Evaluate side-chains 182 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 239 ARG Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 11 LYS Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 210 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 89 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 32 optimal weight: 7.9990 chunk 116 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 3 optimal weight: 0.0870 chunk 135 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.122983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.102971 restraints weight = 16392.001| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.50 r_work: 0.3014 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14827 Z= 0.113 Angle : 0.469 5.805 20125 Z= 0.240 Chirality : 0.042 0.236 2321 Planarity : 0.003 0.033 2593 Dihedral : 10.314 85.501 2269 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.81 % Allowed : 15.19 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.20), residues: 1886 helix: 1.59 (0.18), residues: 828 sheet: -0.29 (0.26), residues: 395 loop : 0.16 (0.26), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 236 TYR 0.016 0.001 TYR C 4 PHE 0.011 0.001 PHE A 378 TRP 0.009 0.001 TRP A 12 HIS 0.002 0.000 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00259 (14827) covalent geometry : angle 0.46934 (20125) hydrogen bonds : bond 0.03491 ( 734) hydrogen bonds : angle 4.33717 ( 2067) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 171 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7906 (tp30) cc_final: 0.7615 (mm-30) REVERT: A 36 MET cc_start: 0.8825 (mtp) cc_final: 0.8549 (mtp) REVERT: A 123 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8170 (mt-10) REVERT: A 174 MET cc_start: 0.8836 (mmm) cc_final: 0.8452 (mmm) REVERT: A 247 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8312 (mtt) REVERT: A 261 ASP cc_start: 0.8538 (p0) cc_final: 0.8333 (p0) REVERT: A 317 ASP cc_start: 0.7355 (m-30) cc_final: 0.7050 (m-30) REVERT: A 369 ASP cc_start: 0.8142 (m-30) cc_final: 0.7742 (m-30) REVERT: A 391 GLU cc_start: 0.8087 (mp0) cc_final: 0.7693 (mp0) REVERT: A 421 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7622 (tm-30) REVERT: A 457 LYS cc_start: 0.8440 (tptt) cc_final: 0.7799 (ttpt) REVERT: B 13 LYS cc_start: 0.8288 (mtpm) cc_final: 0.7204 (mttt) REVERT: B 120 GLN cc_start: 0.8525 (mt0) cc_final: 0.7989 (mp10) REVERT: B 174 MET cc_start: 0.8596 (mmm) cc_final: 0.7968 (mmm) REVERT: B 208 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.6927 (tpp-160) REVERT: B 293 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7871 (mm-30) REVERT: B 331 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7871 (m-30) REVERT: B 368 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7822 (ptmm) REVERT: B 401 GLU cc_start: 0.7273 (mp0) cc_final: 0.6817 (pt0) REVERT: B 421 GLU cc_start: 0.8086 (pp20) cc_final: 0.7678 (mt-10) REVERT: C 11 LYS cc_start: 0.7693 (pmtt) cc_final: 0.7387 (ptpt) REVERT: C 17 GLN cc_start: 0.7284 (mp10) cc_final: 0.6599 (mp-120) REVERT: C 122 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8667 (mtm) REVERT: C 214 ASP cc_start: 0.8544 (m-30) cc_final: 0.8330 (m-30) REVERT: C 220 LYS cc_start: 0.8162 (mppt) cc_final: 0.7625 (mppt) REVERT: C 235 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7225 (mm-30) REVERT: C 239 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6695 (mtm110) REVERT: C 368 LYS cc_start: 0.7950 (mtmm) cc_final: 0.7580 (ptpp) REVERT: C 461 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7514 (tt0) REVERT: D 1 MET cc_start: 0.5971 (tpp) cc_final: 0.5559 (ttp) REVERT: D 11 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.7336 (ptpt) REVERT: D 75 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7749 (mm-30) REVERT: D 214 ASP cc_start: 0.7629 (m-30) cc_final: 0.7072 (p0) REVERT: D 220 LYS cc_start: 0.8239 (mppt) cc_final: 0.7798 (mmtm) REVERT: D 263 ASP cc_start: 0.8361 (t0) cc_final: 0.7995 (t70) REVERT: D 269 LYS cc_start: 0.7921 (mttt) cc_final: 0.7544 (mtmm) REVERT: D 305 GLU cc_start: 0.6741 (pt0) cc_final: 0.6510 (pt0) REVERT: D 352 LYS cc_start: 0.7855 (tttt) cc_final: 0.7560 (tttt) REVERT: D 421 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7741 (mm-30) outliers start: 27 outliers final: 13 residues processed: 181 average time/residue: 0.8879 time to fit residues: 172.3263 Evaluate side-chains 180 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 239 ARG Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 11 LYS Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 210 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 93 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 174 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.117595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.096693 restraints weight = 16568.624| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.61 r_work: 0.2962 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14827 Z= 0.193 Angle : 0.541 5.752 20125 Z= 0.275 Chirality : 0.044 0.230 2321 Planarity : 0.004 0.034 2593 Dihedral : 10.866 87.692 2269 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.47 % Allowed : 15.86 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.20), residues: 1886 helix: 1.38 (0.18), residues: 827 sheet: -0.41 (0.27), residues: 365 loop : 0.11 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 236 TYR 0.021 0.002 TYR C 4 PHE 0.013 0.002 PHE A 413 TRP 0.011 0.002 TRP C 359 HIS 0.002 0.001 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00467 (14827) covalent geometry : angle 0.54085 (20125) hydrogen bonds : bond 0.03999 ( 734) hydrogen bonds : angle 4.52756 ( 2067) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.616 Fit side-chains REVERT: A 16 GLU cc_start: 0.7943 (tp30) cc_final: 0.7654 (mm-30) REVERT: A 36 MET cc_start: 0.8836 (mtp) cc_final: 0.8560 (mtp) REVERT: A 123 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8286 (mt-10) REVERT: A 174 MET cc_start: 0.8885 (mmm) cc_final: 0.8409 (mmm) REVERT: A 247 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8388 (mtt) REVERT: A 317 ASP cc_start: 0.7391 (m-30) cc_final: 0.7067 (m-30) REVERT: A 391 GLU cc_start: 0.8124 (mp0) cc_final: 0.7867 (mp0) REVERT: A 421 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7710 (tm-30) REVERT: A 457 LYS cc_start: 0.8476 (tptt) cc_final: 0.7849 (ttpt) REVERT: B 13 LYS cc_start: 0.8395 (mtpm) cc_final: 0.7339 (mttt) REVERT: B 120 GLN cc_start: 0.8609 (mt0) cc_final: 0.8064 (mp10) REVERT: B 174 MET cc_start: 0.8646 (mmm) cc_final: 0.8012 (mmm) REVERT: B 208 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7182 (tpp-160) REVERT: B 211 GLU cc_start: 0.7597 (pt0) cc_final: 0.7369 (mt-10) REVERT: B 368 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7880 (ptmm) REVERT: B 401 GLU cc_start: 0.7497 (mp0) cc_final: 0.6992 (pt0) REVERT: B 421 GLU cc_start: 0.8049 (pp20) cc_final: 0.7552 (mt-10) REVERT: C 11 LYS cc_start: 0.7809 (pmtt) cc_final: 0.7362 (ptpt) REVERT: C 17 GLN cc_start: 0.7323 (mp10) cc_final: 0.6627 (mp-120) REVERT: C 214 ASP cc_start: 0.8626 (m-30) cc_final: 0.8392 (m-30) REVERT: C 220 LYS cc_start: 0.8203 (mppt) cc_final: 0.7663 (mppt) REVERT: C 235 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7356 (mm-30) REVERT: C 239 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6798 (mtm110) REVERT: C 368 LYS cc_start: 0.8008 (mtmm) cc_final: 0.7634 (ptpp) REVERT: C 461 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7481 (tt0) REVERT: D 1 MET cc_start: 0.6195 (tpp) cc_final: 0.5894 (ttp) REVERT: D 11 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7353 (ptpt) REVERT: D 75 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7866 (mm-30) REVERT: D 214 ASP cc_start: 0.8027 (m-30) cc_final: 0.7290 (p0) REVERT: D 220 LYS cc_start: 0.8277 (mppt) cc_final: 0.7797 (mmtm) REVERT: D 263 ASP cc_start: 0.8395 (t0) cc_final: 0.8025 (t70) REVERT: D 269 LYS cc_start: 0.8091 (mttt) cc_final: 0.7716 (mtmm) REVERT: D 305 GLU cc_start: 0.6770 (pt0) cc_final: 0.6550 (pt0) REVERT: D 352 LYS cc_start: 0.7916 (tttt) cc_final: 0.7715 (tttt) REVERT: D 421 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7714 (mm-30) outliers start: 22 outliers final: 12 residues processed: 172 average time/residue: 0.8911 time to fit residues: 164.2732 Evaluate side-chains 177 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 368 LYS Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 239 ARG Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 11 LYS Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 210 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 14 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 105 optimal weight: 7.9990 chunk 182 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 166 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 chunk 145 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.118742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.097920 restraints weight = 16468.162| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.61 r_work: 0.2987 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14827 Z= 0.148 Angle : 0.507 5.829 20125 Z= 0.258 Chirality : 0.043 0.254 2321 Planarity : 0.004 0.033 2593 Dihedral : 10.634 89.326 2269 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.41 % Allowed : 16.00 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.20), residues: 1886 helix: 1.47 (0.18), residues: 824 sheet: -0.31 (0.27), residues: 395 loop : 0.08 (0.26), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 236 TYR 0.018 0.001 TYR C 4 PHE 0.012 0.001 PHE A 378 TRP 0.009 0.001 TRP A 12 HIS 0.002 0.001 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00353 (14827) covalent geometry : angle 0.50658 (20125) hydrogen bonds : bond 0.03765 ( 734) hydrogen bonds : angle 4.46422 ( 2067) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4941.79 seconds wall clock time: 85 minutes 32.46 seconds (5132.46 seconds total)