Starting phenix.real_space_refine on Mon Apr 6 19:24:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uuh_64511/04_2026/9uuh_64511_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uuh_64511/04_2026/9uuh_64511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uuh_64511/04_2026/9uuh_64511_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uuh_64511/04_2026/9uuh_64511_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uuh_64511/04_2026/9uuh_64511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uuh_64511/04_2026/9uuh_64511.map" } resolution = 3.07 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= 0.001 sd= 0.026 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 48 5.16 5 C 13436 2.51 5 N 3708 2.21 5 O 3796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21000 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 632, 5219 Classifications: {'peptide': 632} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 605} Chain breaks: 4 Chain: "B" Number of atoms: 5219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 632, 5219 Classifications: {'peptide': 632} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 605} Chain breaks: 4 Chain: "C" Number of atoms: 5219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 632, 5219 Classifications: {'peptide': 632} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 605} Chain breaks: 4 Chain: "D" Number of atoms: 5219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 632, 5219 Classifications: {'peptide': 632} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 605} Chain breaks: 4 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.65, per 1000 atoms: 0.22 Number of scatterers: 21000 At special positions: 0 Unit cell: (105.651, 141.687, 127.764, 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 48 16.00 P 12 15.00 O 3796 8.00 N 3708 7.00 C 13436 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: 1.52 Conformation dependent library (CDL) restraints added in 887.1 milliseconds 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4864 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 22 sheets defined 44.9% alpha, 19.1% 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 9 through 26 removed outlier: 3.582A pdb=" N GLU A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA A 25 " --> pdb=" O VAL A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 68 removed outlier: 4.284A pdb=" N PHE A 54 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ALA A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 56 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 104 removed outlier: 3.732A pdb=" N ARG A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 131 removed outlier: 3.751A pdb=" N SER A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 135 Processing helix chain 'A' and resid 145 through 150 removed outlier: 4.041A pdb=" N PHE A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 212 removed outlier: 5.491A pdb=" N ASP A 208 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ASP A 209 " --> pdb=" O TYR A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 281 Processing helix chain 'A' and resid 296 through 303 removed outlier: 3.534A pdb=" N ASN A 302 " --> pdb=" O ASP A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 331 through 339 removed outlier: 3.649A pdb=" N ALA A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 363 removed outlier: 3.672A pdb=" N LEU A 354 " --> pdb=" O PHE A 350 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 392 removed outlier: 3.564A pdb=" N ASP A 384 " --> pdb=" O SER A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 466 Processing helix chain 'A' and resid 477 through 493 removed outlier: 3.780A pdb=" N GLU A 483 " --> pdb=" O ARG A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 527 removed outlier: 3.566A pdb=" N GLN A 527 " --> pdb=" O ALA A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 555 Processing helix chain 'A' and resid 600 through 603 removed outlier: 3.852A pdb=" N ASP A 603 " --> pdb=" O ASN A 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 600 through 603' Processing helix chain 'A' and resid 614 through 620 Processing helix chain 'A' and resid 630 through 646 Processing helix chain 'A' and resid 675 through 685 Processing helix chain 'B' and resid 9 through 26 removed outlier: 3.582A pdb=" N GLU B 24 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA B 25 " --> pdb=" O VAL B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 68 removed outlier: 4.284A pdb=" N PHE B 54 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ALA B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU B 56 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN B 67 " --> pdb=" O ILE B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 104 removed outlier: 3.732A pdb=" N ARG B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 131 removed outlier: 3.751A pdb=" N SER B 121 " --> pdb=" O ALA B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 135 Processing helix chain 'B' and resid 145 through 150 removed outlier: 4.041A pdb=" N PHE B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 removed outlier: 5.491A pdb=" N ASP B 208 " --> pdb=" O ARG B 204 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ASP B 209 " --> pdb=" O TYR B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 281 Processing helix chain 'B' and resid 296 through 303 removed outlier: 3.534A pdb=" N ASN B 302 " --> pdb=" O ASP B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'B' and resid 321 through 326 Processing helix chain 'B' and resid 331 through 339 removed outlier: 3.649A pdb=" N ALA B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 363 removed outlier: 3.672A pdb=" N LEU B 354 " --> pdb=" O PHE B 350 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE B 362 " --> pdb=" O ARG B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 392 removed outlier: 3.564A pdb=" N ASP B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 466 Processing helix chain 'B' and resid 477 through 493 removed outlier: 3.780A pdb=" N GLU B 483 " --> pdb=" O ARG B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 527 removed outlier: 3.566A pdb=" N GLN B 527 " --> pdb=" O ALA B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 555 Processing helix chain 'B' and resid 600 through 603 removed outlier: 3.852A pdb=" N ASP B 603 " --> pdb=" O ASN B 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 600 through 603' Processing helix chain 'B' and resid 614 through 620 Processing helix chain 'B' and resid 630 through 646 Processing helix chain 'B' and resid 675 through 685 Processing helix chain 'C' and resid 9 through 26 Processing helix chain 'C' and resid 31 through 52 removed outlier: 3.635A pdb=" N GLY C 40 " --> pdb=" O MET C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 67 Processing helix chain 'C' and resid 74 through 104 removed outlier: 3.671A pdb=" N ALA C 103 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG C 104 " --> pdb=" O LEU C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 131 Processing helix chain 'C' and resid 145 through 150 removed outlier: 4.551A pdb=" N PHE C 149 " --> pdb=" O ASP C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 206 Processing helix chain 'C' and resid 207 through 212 removed outlier: 3.502A pdb=" N PHE C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 280 Processing helix chain 'C' and resid 296 through 303 removed outlier: 3.718A pdb=" N ILE C 301 " --> pdb=" O LYS C 298 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN C 302 " --> pdb=" O ASP C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 312 removed outlier: 3.627A pdb=" N LEU C 311 " --> pdb=" O LYS C 308 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL C 312 " --> pdb=" O ALA C 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 308 through 312' Processing helix chain 'C' and resid 331 through 339 removed outlier: 3.846A pdb=" N ALA C 335 " --> pdb=" O ASN C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 363 removed outlier: 3.558A pdb=" N LEU C 354 " --> pdb=" O PHE C 350 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE C 362 " --> pdb=" O ARG C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 392 Processing helix chain 'C' and resid 463 through 466 Processing helix chain 'C' and resid 477 through 493 removed outlier: 4.061A pdb=" N GLU C 483 " --> pdb=" O ARG C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 527 removed outlier: 3.531A pdb=" N LEU C 513 " --> pdb=" O ASN C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 556 Processing helix chain 'C' and resid 600 through 603 removed outlier: 3.707A pdb=" N ASP C 603 " --> pdb=" O ASN C 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 600 through 603' Processing helix chain 'C' and resid 614 through 620 Processing helix chain 'C' and resid 630 through 646 Processing helix chain 'C' and resid 673 through 685 removed outlier: 3.749A pdb=" N TYR C 678 " --> pdb=" O GLN C 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 26 Processing helix chain 'D' and resid 31 through 52 removed outlier: 3.635A pdb=" N GLY D 40 " --> pdb=" O MET D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 67 Processing helix chain 'D' and resid 74 through 104 removed outlier: 3.671A pdb=" N ALA D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 131 Processing helix chain 'D' and resid 145 through 150 removed outlier: 4.551A pdb=" N PHE D 149 " --> pdb=" O ASP D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 206 Processing helix chain 'D' and resid 207 through 212 removed outlier: 3.502A pdb=" N PHE D 211 " --> pdb=" O LEU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 280 Processing helix chain 'D' and resid 296 through 303 removed outlier: 3.718A pdb=" N ILE D 301 " --> pdb=" O LYS D 298 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN D 302 " --> pdb=" O ASP D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 312 removed outlier: 3.627A pdb=" N LEU D 311 " --> pdb=" O LYS D 308 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL D 312 " --> pdb=" O ALA D 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 312' Processing helix chain 'D' and resid 331 through 339 removed outlier: 3.846A pdb=" N ALA D 335 " --> pdb=" O ASN D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 363 removed outlier: 3.558A pdb=" N LEU D 354 " --> pdb=" O PHE D 350 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE D 362 " --> pdb=" O ARG D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 392 Processing helix chain 'D' and resid 463 through 466 Processing helix chain 'D' and resid 477 through 493 removed outlier: 4.061A pdb=" N GLU D 483 " --> pdb=" O ARG D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 527 removed outlier: 3.531A pdb=" N LEU D 513 " --> pdb=" O ASN D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 556 Processing helix chain 'D' and resid 600 through 603 removed outlier: 3.707A pdb=" N ASP D 603 " --> pdb=" O ASN D 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 600 through 603' Processing helix chain 'D' and resid 614 through 620 Processing helix chain 'D' and resid 630 through 646 Processing helix chain 'D' and resid 673 through 685 removed outlier: 3.749A pdb=" N TYR D 678 " --> pdb=" O GLN D 674 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 110 removed outlier: 6.249A pdb=" N PHE A 108 " --> pdb=" O MET A 196 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU A 198 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N ILE A 110 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 140 removed outlier: 4.853A pdb=" N TYR A 169 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA A 219 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A 228 " --> pdb=" O ARG A 261 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL A 260 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL A 289 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N PHE A 262 " --> pdb=" O VAL A 289 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 341 through 345 removed outlier: 4.311A pdb=" N LYS A 437 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU A 438 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ILE A 371 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU A 440 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE A 369 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N SER A 442 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU A 367 " --> pdb=" O LYS A 395 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N THR A 397 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE A 369 " --> pdb=" O THR A 397 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL A 399 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE A 371 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL A 396 " --> pdb=" O HIS A 424 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ILE A 426 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL A 398 " --> pdb=" O ILE A 426 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 345 Processing sheet with id=AA5, first strand: chain 'A' and resid 433 through 434 removed outlier: 7.180A pdb=" N LYS A 433 " --> pdb=" O ILE A 622 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 504 through 505 removed outlier: 3.994A pdb=" N ARG A 594 " --> pdb=" O SER A 609 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE A 533 " --> pdb=" O ASN A 560 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LEU A 562 " --> pdb=" O ILE A 533 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU A 535 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE A 585 " --> pdb=" O ILE A 563 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 107 through 110 removed outlier: 6.249A pdb=" N PHE B 108 " --> pdb=" O MET B 196 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU B 198 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N ILE B 110 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 138 through 140 removed outlier: 4.853A pdb=" N TYR B 169 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA B 219 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR B 228 " --> pdb=" O ARG B 261 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL B 260 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL B 289 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N PHE B 262 " --> pdb=" O VAL B 289 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 341 through 345 removed outlier: 4.311A pdb=" N LYS B 437 " --> pdb=" O GLY B 456 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU B 438 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ILE B 371 " --> pdb=" O LEU B 438 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU B 440 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE B 369 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N SER B 442 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU B 367 " --> pdb=" O LYS B 395 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N THR B 397 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE B 369 " --> pdb=" O THR B 397 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL B 399 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE B 371 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL B 396 " --> pdb=" O HIS B 424 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ILE B 426 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL B 398 " --> pdb=" O ILE B 426 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 341 through 345 Processing sheet with id=AB2, first strand: chain 'B' and resid 433 through 434 removed outlier: 7.180A pdb=" N LYS B 433 " --> pdb=" O ILE B 622 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 504 through 505 removed outlier: 3.994A pdb=" N ARG B 594 " --> pdb=" O SER B 609 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE B 533 " --> pdb=" O ASN B 560 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LEU B 562 " --> pdb=" O ILE B 533 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU B 535 " --> pdb=" O LEU B 562 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE B 585 " --> pdb=" O ILE B 563 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 107 through 109 removed outlier: 6.382A pdb=" N PHE C 108 " --> pdb=" O MET C 196 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N LEU C 198 " --> pdb=" O PHE C 108 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 138 through 139 removed outlier: 4.409A pdb=" N TYR C 154 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N MET C 227 " --> pdb=" O TYR C 154 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 219 " --> pdb=" O ILE C 162 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 341 through 345 removed outlier: 4.496A pdb=" N LYS C 437 " --> pdb=" O GLY C 456 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU C 438 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ILE C 371 " --> pdb=" O LEU C 438 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU C 440 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE C 369 " --> pdb=" O LEU C 440 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER C 442 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL C 396 " --> pdb=" O HIS C 424 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ILE C 426 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL C 398 " --> pdb=" O ILE C 426 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 341 through 345 Processing sheet with id=AB8, first strand: chain 'C' and resid 504 through 505 removed outlier: 4.148A pdb=" N ARG C 594 " --> pdb=" O SER C 609 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE C 533 " --> pdb=" O ASN C 560 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU C 562 " --> pdb=" O ILE C 533 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU C 535 " --> pdb=" O LEU C 562 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 107 through 109 removed outlier: 6.382A pdb=" N PHE D 108 " --> pdb=" O MET D 196 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N LEU D 198 " --> pdb=" O PHE D 108 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 138 through 139 removed outlier: 4.409A pdb=" N TYR D 154 " --> pdb=" O MET D 227 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N MET D 227 " --> pdb=" O TYR D 154 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA D 219 " --> pdb=" O ILE D 162 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 341 through 345 removed outlier: 4.496A pdb=" N LYS D 437 " --> pdb=" O GLY D 456 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU D 438 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ILE D 371 " --> pdb=" O LEU D 438 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU D 440 " --> pdb=" O ILE D 369 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE D 369 " --> pdb=" O LEU D 440 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER D 442 " --> pdb=" O LEU D 367 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL D 396 " --> pdb=" O HIS D 424 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ILE D 426 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL D 398 " --> pdb=" O ILE D 426 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 341 through 345 Processing sheet with id=AC4, first strand: chain 'D' and resid 504 through 505 removed outlier: 4.148A pdb=" N ARG D 594 " --> pdb=" O SER D 609 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE D 533 " --> pdb=" O ASN D 560 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU D 562 " --> pdb=" O ILE D 533 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU D 535 " --> pdb=" O LEU D 562 " (cutoff:3.500A) 1016 hydrogen bonds defined for protein. 2868 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: 3.86 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6930 1.34 - 1.46: 4550 1.46 - 1.58: 9840 1.58 - 1.70: 20 1.70 - 1.82: 88 Bond restraints: 21428 Sorted by residual: bond pdb=" N PRO D 269 " pdb=" CD PRO D 269 " ideal model delta sigma weight residual 1.473 1.425 0.048 1.40e-02 5.10e+03 1.17e+01 bond pdb=" N PRO C 269 " pdb=" CD PRO C 269 " ideal model delta sigma weight residual 1.473 1.425 0.048 1.40e-02 5.10e+03 1.17e+01 bond pdb=" N ILE D 197 " pdb=" CA ILE D 197 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.19e-02 7.06e+03 7.66e+00 bond pdb=" N ILE C 197 " pdb=" CA ILE C 197 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.19e-02 7.06e+03 7.66e+00 bond pdb=" N ILE C 202 " pdb=" CA ILE C 202 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.23e-02 6.61e+03 7.57e+00 ... (remaining 21423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 28338 1.49 - 2.97: 520 2.97 - 4.46: 88 4.46 - 5.95: 24 5.95 - 7.43: 14 Bond angle restraints: 28984 Sorted by residual: angle pdb=" N ARG D 204 " pdb=" CA ARG D 204 " pdb=" C ARG D 204 " ideal model delta sigma weight residual 113.88 107.84 6.04 1.23e+00 6.61e-01 2.41e+01 angle pdb=" N ARG C 204 " pdb=" CA ARG C 204 " pdb=" C ARG C 204 " ideal model delta sigma weight residual 113.88 107.84 6.04 1.23e+00 6.61e-01 2.41e+01 angle pdb=" N GLU C 420 " pdb=" CA GLU C 420 " pdb=" C GLU C 420 " ideal model delta sigma weight residual 111.07 106.00 5.07 1.07e+00 8.73e-01 2.25e+01 angle pdb=" N GLU D 420 " pdb=" CA GLU D 420 " pdb=" C GLU D 420 " ideal model delta sigma weight residual 111.07 106.00 5.07 1.07e+00 8.73e-01 2.25e+01 angle pdb=" N LEU C 207 " pdb=" CA LEU C 207 " pdb=" C LEU C 207 " ideal model delta sigma weight residual 112.90 107.21 5.69 1.31e+00 5.83e-01 1.88e+01 ... (remaining 28979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 11178 17.80 - 35.61: 1454 35.61 - 53.41: 384 53.41 - 71.21: 80 71.21 - 89.02: 36 Dihedral angle restraints: 13132 sinusoidal: 5628 harmonic: 7504 Sorted by residual: dihedral pdb=" CD ARG D 142 " pdb=" NE ARG D 142 " pdb=" CZ ARG D 142 " pdb=" NH1 ARG D 142 " ideal model delta sinusoidal sigma weight residual 0.00 89.02 -89.02 1 1.00e+01 1.00e-02 9.44e+01 dihedral pdb=" CD ARG C 142 " pdb=" NE ARG C 142 " pdb=" CZ ARG C 142 " pdb=" NH1 ARG C 142 " ideal model delta sinusoidal sigma weight residual 0.00 89.02 -89.02 1 1.00e+01 1.00e-02 9.44e+01 dihedral pdb=" CA LEU A 438 " pdb=" C LEU A 438 " pdb=" N PHE A 439 " pdb=" CA PHE A 439 " ideal model delta harmonic sigma weight residual 180.00 158.42 21.58 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 13129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2740 0.060 - 0.121: 426 0.121 - 0.181: 38 0.181 - 0.241: 2 0.241 - 0.302: 2 Chirality restraints: 3208 Sorted by residual: chirality pdb=" CA ILE D 138 " pdb=" N ILE D 138 " pdb=" C ILE D 138 " pdb=" CB ILE D 138 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CA ILE C 138 " pdb=" N ILE C 138 " pdb=" C ILE C 138 " pdb=" CB ILE C 138 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CA LEU D 207 " pdb=" N LEU D 207 " pdb=" C LEU D 207 " pdb=" CB LEU D 207 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.32e-01 ... (remaining 3205 not shown) Planarity restraints: 3708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 142 " 1.100 9.50e-02 1.11e+02 4.93e-01 1.46e+02 pdb=" NE ARG D 142 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG D 142 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG D 142 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG D 142 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 142 " 1.100 9.50e-02 1.11e+02 4.93e-01 1.46e+02 pdb=" NE ARG C 142 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG C 142 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C 142 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG C 142 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 204 " -0.545 9.50e-02 1.11e+02 2.44e-01 3.65e+01 pdb=" NE ARG C 204 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG C 204 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG C 204 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 204 " -0.018 2.00e-02 2.50e+03 ... (remaining 3705 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1630 2.74 - 3.28: 19956 3.28 - 3.82: 34286 3.82 - 4.36: 41960 4.36 - 4.90: 73394 Nonbonded interactions: 171226 Sorted by model distance: nonbonded pdb=" OG SER A 506 " pdb=" OG SER A 510 " model vdw 2.203 3.040 nonbonded pdb=" OG SER B 506 " pdb=" OG SER B 510 " model vdw 2.203 3.040 nonbonded pdb=" OH TYR D 7 " pdb=" OD1 ASP D 547 " model vdw 2.226 3.040 nonbonded pdb=" OH TYR C 7 " pdb=" OD1 ASP C 547 " model vdw 2.226 3.040 nonbonded pdb=" OH TYR A 154 " pdb=" OD2 ASP A 177 " model vdw 2.228 3.040 ... (remaining 171221 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 18.780 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 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 : 0.004 0.048 21428 Z= 0.183 Angle : 0.528 7.434 28984 Z= 0.316 Chirality : 0.045 0.302 3208 Planarity : 0.013 0.493 3708 Dihedral : 17.539 89.018 8268 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.00 % Allowed : 21.10 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.17), residues: 2488 helix: 1.97 (0.16), residues: 968 sheet: -0.37 (0.23), residues: 520 loop : 0.18 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 581 TYR 0.008 0.001 TYR C 596 PHE 0.025 0.001 PHE A 439 TRP 0.006 0.001 TRP C 14 HIS 0.003 0.000 HIS B 454 Details of bonding type rmsd covalent geometry : bond 0.00369 (21428) covalent geometry : angle 0.52818 (28984) hydrogen bonds : bond 0.17368 ( 992) hydrogen bonds : angle 6.97012 ( 2868) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.799 Fit side-chains REVERT: A 395 LYS cc_start: 0.8342 (mmtm) cc_final: 0.8103 (mttt) REVERT: B 395 LYS cc_start: 0.8342 (mmtm) cc_final: 0.8105 (mttt) REVERT: C 138 ILE cc_start: 0.8515 (mt) cc_final: 0.8195 (mm) REVERT: D 138 ILE cc_start: 0.8517 (mt) cc_final: 0.8197 (mm) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1668 time to fit residues: 44.9134 Evaluate side-chains 166 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 GLN C 114 GLN C 529 GLN D 23 GLN D 529 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.124942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.103925 restraints weight = 28149.124| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.03 r_work: 0.3118 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.0776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21428 Z= 0.148 Angle : 0.459 7.045 28984 Z= 0.247 Chirality : 0.042 0.181 3208 Planarity : 0.003 0.029 3708 Dihedral : 9.195 86.009 2996 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.10 % Allowed : 19.79 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.17), residues: 2488 helix: 2.11 (0.16), residues: 1000 sheet: -0.41 (0.23), residues: 528 loop : 0.27 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 337 TYR 0.010 0.001 TYR B 680 PHE 0.029 0.001 PHE B 439 TRP 0.008 0.001 TRP A 122 HIS 0.003 0.001 HIS D 454 Details of bonding type rmsd covalent geometry : bond 0.00344 (21428) covalent geometry : angle 0.45903 (28984) hydrogen bonds : bond 0.04013 ( 992) hydrogen bonds : angle 4.86842 ( 2868) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 194 time to evaluate : 0.816 Fit side-chains REVERT: A 395 LYS cc_start: 0.8277 (mmtm) cc_final: 0.7950 (mttt) REVERT: A 623 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8252 (mt-10) REVERT: B 395 LYS cc_start: 0.8279 (mmtm) cc_final: 0.7945 (mttt) REVERT: B 623 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8256 (mt-10) REVERT: C 145 ASP cc_start: 0.7946 (p0) cc_final: 0.7525 (p0) REVERT: C 154 TYR cc_start: 0.8305 (m-80) cc_final: 0.8098 (m-80) REVERT: C 227 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8342 (tpt) REVERT: C 447 ASP cc_start: 0.7724 (t70) cc_final: 0.7510 (t0) REVERT: C 477 ASP cc_start: 0.7971 (t0) cc_final: 0.7714 (t0) REVERT: D 145 ASP cc_start: 0.7953 (p0) cc_final: 0.7519 (p0) REVERT: D 154 TYR cc_start: 0.8279 (m-80) cc_final: 0.8066 (m-80) REVERT: D 227 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8335 (tpt) REVERT: D 447 ASP cc_start: 0.7714 (t70) cc_final: 0.7500 (t0) REVERT: D 477 ASP cc_start: 0.7987 (t0) cc_final: 0.7724 (t0) outliers start: 48 outliers final: 26 residues processed: 228 average time/residue: 0.1605 time to fit residues: 56.0600 Evaluate side-chains 198 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 297 PHE Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 297 PHE Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 569 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 215 optimal weight: 0.3980 chunk 179 optimal weight: 0.0060 chunk 159 optimal weight: 0.1980 chunk 110 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 246 optimal weight: 0.6980 chunk 236 optimal weight: 9.9990 chunk 30 optimal weight: 0.6980 chunk 147 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 529 GLN D 529 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.127322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.106502 restraints weight = 27968.157| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.03 r_work: 0.3157 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 21428 Z= 0.089 Angle : 0.413 6.691 28984 Z= 0.223 Chirality : 0.041 0.163 3208 Planarity : 0.003 0.030 3708 Dihedral : 8.852 83.811 2996 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.19 % Allowed : 19.96 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.17), residues: 2488 helix: 2.27 (0.16), residues: 1012 sheet: -0.19 (0.23), residues: 508 loop : 0.32 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 665 TYR 0.008 0.001 TYR D 264 PHE 0.025 0.001 PHE B 439 TRP 0.006 0.001 TRP A 14 HIS 0.007 0.001 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00189 (21428) covalent geometry : angle 0.41323 (28984) hydrogen bonds : bond 0.03168 ( 992) hydrogen bonds : angle 4.47162 ( 2868) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 204 time to evaluate : 0.815 Fit side-chains REVERT: A 395 LYS cc_start: 0.8204 (mmtm) cc_final: 0.7837 (mtmt) REVERT: A 447 ASP cc_start: 0.7843 (t70) cc_final: 0.7540 (t0) REVERT: A 517 MET cc_start: 0.8319 (mtp) cc_final: 0.7999 (mtt) REVERT: A 623 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8178 (mt-10) REVERT: B 395 LYS cc_start: 0.8213 (mmtm) cc_final: 0.7840 (mtmt) REVERT: B 447 ASP cc_start: 0.7855 (t70) cc_final: 0.7547 (t0) REVERT: B 517 MET cc_start: 0.8331 (mtp) cc_final: 0.8011 (mtt) REVERT: B 623 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8199 (mt-10) REVERT: C 145 ASP cc_start: 0.7948 (p0) cc_final: 0.7560 (p0) REVERT: C 227 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8349 (tpt) REVERT: C 447 ASP cc_start: 0.7853 (t70) cc_final: 0.7575 (t0) REVERT: C 477 ASP cc_start: 0.7885 (t0) cc_final: 0.7616 (t0) REVERT: C 621 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7972 (ttm170) REVERT: D 145 ASP cc_start: 0.7961 (p0) cc_final: 0.7555 (p0) REVERT: D 227 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8330 (tpt) REVERT: D 447 ASP cc_start: 0.7867 (t70) cc_final: 0.7587 (t0) REVERT: D 477 ASP cc_start: 0.7902 (t0) cc_final: 0.7627 (t0) REVERT: D 621 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7975 (ttm170) outliers start: 50 outliers final: 22 residues processed: 238 average time/residue: 0.1651 time to fit residues: 59.5861 Evaluate side-chains 206 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 297 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 621 ARG Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 297 PHE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 621 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 126 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 236 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 chunk 13 optimal weight: 5.9990 chunk 249 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS B 388 HIS C 539 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.125263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.104377 restraints weight = 28253.368| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.03 r_work: 0.3122 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 21428 Z= 0.153 Angle : 0.452 7.220 28984 Z= 0.238 Chirality : 0.042 0.166 3208 Planarity : 0.003 0.027 3708 Dihedral : 8.848 89.206 2996 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.98 % Allowed : 19.53 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.17), residues: 2488 helix: 2.23 (0.16), residues: 1012 sheet: -0.15 (0.23), residues: 508 loop : 0.29 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 358 TYR 0.009 0.001 TYR A 130 PHE 0.029 0.001 PHE B 439 TRP 0.006 0.001 TRP D 613 HIS 0.004 0.001 HIS A 454 Details of bonding type rmsd covalent geometry : bond 0.00364 (21428) covalent geometry : angle 0.45219 (28984) hydrogen bonds : bond 0.03477 ( 992) hydrogen bonds : angle 4.43112 ( 2868) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 186 time to evaluate : 0.814 Fit side-chains REVERT: A 395 LYS cc_start: 0.8265 (mmtm) cc_final: 0.7871 (mttt) REVERT: A 623 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8196 (mt-10) REVERT: A 661 ARG cc_start: 0.8387 (ttp80) cc_final: 0.8183 (tmm160) REVERT: B 395 LYS cc_start: 0.8274 (mmtm) cc_final: 0.7879 (mttt) REVERT: B 623 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8195 (mt-10) REVERT: B 661 ARG cc_start: 0.8387 (ttp80) cc_final: 0.8182 (tmm160) REVERT: C 227 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8396 (tpt) REVERT: C 447 ASP cc_start: 0.7921 (t70) cc_final: 0.7602 (t0) REVERT: C 621 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.8049 (mtt-85) REVERT: C 674 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.7160 (mm-40) REVERT: D 227 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8394 (tpt) REVERT: D 447 ASP cc_start: 0.7919 (t70) cc_final: 0.7600 (t0) REVERT: D 621 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.8062 (mtt-85) REVERT: D 674 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.7140 (mm-40) outliers start: 68 outliers final: 50 residues processed: 234 average time/residue: 0.1597 time to fit residues: 57.1838 Evaluate side-chains 228 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 170 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 297 PHE Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 621 ARG Chi-restraints excluded: chain C residue 674 GLN Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 297 PHE Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 621 ARG Chi-restraints excluded: chain D residue 674 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 21 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 243 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 205 optimal weight: 0.2980 chunk 83 optimal weight: 0.8980 chunk 77 optimal weight: 0.0980 chunk 41 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN B 310 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.126838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.106056 restraints weight = 28022.756| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.03 r_work: 0.3152 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 21428 Z= 0.101 Angle : 0.418 6.836 28984 Z= 0.224 Chirality : 0.041 0.161 3208 Planarity : 0.003 0.025 3708 Dihedral : 8.564 85.162 2996 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.71 % Allowed : 20.05 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.17), residues: 2488 helix: 2.33 (0.16), residues: 1012 sheet: -0.05 (0.23), residues: 508 loop : 0.34 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 337 TYR 0.009 0.001 TYR D 264 PHE 0.026 0.001 PHE A 439 TRP 0.005 0.001 TRP A 14 HIS 0.003 0.000 HIS B 125 Details of bonding type rmsd covalent geometry : bond 0.00230 (21428) covalent geometry : angle 0.41801 (28984) hydrogen bonds : bond 0.03016 ( 992) hydrogen bonds : angle 4.28542 ( 2868) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 185 time to evaluate : 0.889 Fit side-chains REVERT: A 54 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.7773 (t80) REVERT: A 395 LYS cc_start: 0.8241 (mmtm) cc_final: 0.7797 (mtmt) REVERT: A 517 MET cc_start: 0.8347 (mtp) cc_final: 0.7944 (mtt) REVERT: A 623 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8171 (mt-10) REVERT: B 54 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.7771 (t80) REVERT: B 395 LYS cc_start: 0.8238 (mmtm) cc_final: 0.7790 (mtmt) REVERT: B 517 MET cc_start: 0.8343 (mtp) cc_final: 0.7942 (mtt) REVERT: B 623 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8183 (mt-10) REVERT: C 145 ASP cc_start: 0.7976 (p0) cc_final: 0.7667 (p0) REVERT: C 447 ASP cc_start: 0.7877 (t70) cc_final: 0.7463 (t0) REVERT: C 674 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.7123 (mm-40) REVERT: D 145 ASP cc_start: 0.7983 (p0) cc_final: 0.7676 (p0) REVERT: D 447 ASP cc_start: 0.7903 (t70) cc_final: 0.7488 (t0) REVERT: D 674 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.7100 (mm-40) outliers start: 62 outliers final: 34 residues processed: 228 average time/residue: 0.1635 time to fit residues: 57.0935 Evaluate side-chains 217 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 297 PHE Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 674 GLN Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 297 PHE Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 674 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 139 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 229 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 61 optimal weight: 0.0070 chunk 83 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 overall best weight: 1.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS B 388 HIS C 529 GLN C 617 ASN D 529 GLN D 617 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.125983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.104956 restraints weight = 27955.790| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.06 r_work: 0.3129 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21428 Z= 0.133 Angle : 0.441 7.182 28984 Z= 0.232 Chirality : 0.042 0.161 3208 Planarity : 0.003 0.026 3708 Dihedral : 8.429 78.708 2996 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.76 % Allowed : 20.10 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.17), residues: 2488 helix: 2.29 (0.16), residues: 1012 sheet: 0.04 (0.23), residues: 508 loop : 0.29 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 616 TYR 0.009 0.001 TYR A 495 PHE 0.028 0.001 PHE A 439 TRP 0.006 0.001 TRP D 613 HIS 0.003 0.001 HIS B 454 Details of bonding type rmsd covalent geometry : bond 0.00315 (21428) covalent geometry : angle 0.44073 (28984) hydrogen bonds : bond 0.03221 ( 992) hydrogen bonds : angle 4.29978 ( 2868) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 187 time to evaluate : 0.784 Fit side-chains REVERT: A 54 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.7813 (t80) REVERT: A 395 LYS cc_start: 0.8243 (mmtm) cc_final: 0.7851 (mtmt) REVERT: B 54 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.7797 (t80) REVERT: B 395 LYS cc_start: 0.8250 (mmtm) cc_final: 0.7847 (mtmt) REVERT: C 145 ASP cc_start: 0.8016 (p0) cc_final: 0.7680 (p0) REVERT: C 447 ASP cc_start: 0.7900 (t70) cc_final: 0.7506 (t0) REVERT: C 485 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8693 (ttp-170) REVERT: C 674 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.7174 (mm-40) REVERT: D 145 ASP cc_start: 0.8023 (p0) cc_final: 0.7690 (p0) REVERT: D 447 ASP cc_start: 0.7902 (t70) cc_final: 0.7512 (t0) REVERT: D 485 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8680 (ttp-170) REVERT: D 674 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.7143 (mm-40) outliers start: 63 outliers final: 53 residues processed: 229 average time/residue: 0.1707 time to fit residues: 58.7895 Evaluate side-chains 237 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 178 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 266 ARG Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 297 PHE Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 485 ARG Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 674 GLN Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 266 ARG Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 297 PHE Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 485 ARG Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 674 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 38 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 208 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 176 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 213 optimal weight: 0.8980 chunk 189 optimal weight: 6.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN B 310 ASN C 529 GLN D 529 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.125853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.104768 restraints weight = 28116.719| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.07 r_work: 0.3126 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21428 Z= 0.133 Angle : 0.444 7.178 28984 Z= 0.234 Chirality : 0.041 0.160 3208 Planarity : 0.003 0.027 3708 Dihedral : 8.293 74.842 2996 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.98 % Allowed : 20.05 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.17), residues: 2488 helix: 2.29 (0.16), residues: 1012 sheet: 0.05 (0.23), residues: 508 loop : 0.28 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 616 TYR 0.008 0.001 TYR B 495 PHE 0.028 0.001 PHE B 439 TRP 0.006 0.001 TRP A 14 HIS 0.003 0.001 HIS A 454 Details of bonding type rmsd covalent geometry : bond 0.00316 (21428) covalent geometry : angle 0.44352 (28984) hydrogen bonds : bond 0.03198 ( 992) hydrogen bonds : angle 4.29575 ( 2868) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 186 time to evaluate : 0.840 Fit side-chains REVERT: A 395 LYS cc_start: 0.8244 (mmtm) cc_final: 0.7847 (mtmt) REVERT: A 447 ASP cc_start: 0.7877 (t70) cc_final: 0.7608 (t0) REVERT: A 616 ARG cc_start: 0.8606 (ptp-110) cc_final: 0.7946 (ptp-110) REVERT: B 395 LYS cc_start: 0.8255 (mmtm) cc_final: 0.7844 (mtmt) REVERT: B 447 ASP cc_start: 0.7906 (t70) cc_final: 0.7639 (t0) REVERT: B 616 ARG cc_start: 0.8614 (ptp-110) cc_final: 0.7959 (ptp-110) REVERT: C 447 ASP cc_start: 0.7924 (t70) cc_final: 0.7545 (t0) REVERT: C 485 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8713 (ttp-170) REVERT: C 674 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.7186 (mm-40) REVERT: D 447 ASP cc_start: 0.7917 (t70) cc_final: 0.7546 (t0) REVERT: D 485 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8700 (ttp-170) REVERT: D 674 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.7159 (mm-40) outliers start: 68 outliers final: 52 residues processed: 234 average time/residue: 0.1664 time to fit residues: 59.8193 Evaluate side-chains 239 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 183 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 266 ARG Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 297 PHE Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 485 ARG Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 674 GLN Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 266 ARG Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 297 PHE Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 485 ARG Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 674 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 56 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 195 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN A 388 HIS B 310 ASN B 388 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.125456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.104342 restraints weight = 27968.812| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.06 r_work: 0.3122 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21428 Z= 0.137 Angle : 0.449 7.234 28984 Z= 0.237 Chirality : 0.042 0.160 3208 Planarity : 0.003 0.027 3708 Dihedral : 8.207 73.610 2996 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.15 % Allowed : 20.05 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.17), residues: 2488 helix: 2.30 (0.16), residues: 1012 sheet: 0.05 (0.23), residues: 508 loop : 0.29 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 616 TYR 0.008 0.001 TYR B 495 PHE 0.028 0.001 PHE B 439 TRP 0.006 0.001 TRP A 14 HIS 0.003 0.001 HIS B 454 Details of bonding type rmsd covalent geometry : bond 0.00327 (21428) covalent geometry : angle 0.44870 (28984) hydrogen bonds : bond 0.03231 ( 992) hydrogen bonds : angle 4.28894 ( 2868) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 182 time to evaluate : 0.640 Fit side-chains REVERT: A 54 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.7822 (t80) REVERT: A 395 LYS cc_start: 0.8259 (mmtm) cc_final: 0.7884 (mttt) REVERT: A 447 ASP cc_start: 0.7908 (t70) cc_final: 0.7655 (t0) REVERT: A 616 ARG cc_start: 0.8575 (ptp-110) cc_final: 0.7919 (ptp-110) REVERT: B 54 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7812 (t80) REVERT: B 395 LYS cc_start: 0.8276 (mmtm) cc_final: 0.7886 (mttt) REVERT: B 447 ASP cc_start: 0.7933 (t70) cc_final: 0.7680 (t0) REVERT: B 616 ARG cc_start: 0.8573 (ptp-110) cc_final: 0.7919 (ptp-110) REVERT: C 145 ASP cc_start: 0.8003 (p0) cc_final: 0.7655 (p0) REVERT: C 447 ASP cc_start: 0.7918 (t70) cc_final: 0.7542 (t0) REVERT: C 485 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8719 (ttp-170) REVERT: C 674 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.7111 (mm-40) REVERT: D 74 ARG cc_start: 0.7022 (mpp-170) cc_final: 0.6818 (mpp-170) REVERT: D 145 ASP cc_start: 0.8015 (p0) cc_final: 0.7660 (p0) REVERT: D 447 ASP cc_start: 0.7899 (t70) cc_final: 0.7529 (t0) REVERT: D 485 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8702 (ttp-170) REVERT: D 674 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.7102 (mm-40) outliers start: 72 outliers final: 66 residues processed: 232 average time/residue: 0.1655 time to fit residues: 58.0663 Evaluate side-chains 247 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 175 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 266 ARG Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 297 PHE Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 485 ARG Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 674 GLN Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 266 ARG Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 297 PHE Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 485 ARG Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 674 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 149 optimal weight: 6.9990 chunk 239 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 156 optimal weight: 0.9990 chunk 247 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 226 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.126230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.105537 restraints weight = 27926.438| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.01 r_work: 0.3142 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21428 Z= 0.112 Angle : 0.438 7.387 28984 Z= 0.232 Chirality : 0.041 0.158 3208 Planarity : 0.003 0.026 3708 Dihedral : 8.093 72.707 2996 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.71 % Allowed : 20.53 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.17), residues: 2488 helix: 2.34 (0.16), residues: 1016 sheet: 0.07 (0.23), residues: 508 loop : 0.32 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 74 TYR 0.007 0.001 TYR C 264 PHE 0.027 0.001 PHE B 439 TRP 0.007 0.001 TRP B 14 HIS 0.003 0.000 HIS C 454 Details of bonding type rmsd covalent geometry : bond 0.00260 (21428) covalent geometry : angle 0.43781 (28984) hydrogen bonds : bond 0.03054 ( 992) hydrogen bonds : angle 4.24001 ( 2868) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 177 time to evaluate : 0.851 Fit side-chains REVERT: A 54 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.7750 (t80) REVERT: A 395 LYS cc_start: 0.8248 (mmtm) cc_final: 0.7793 (mtmt) REVERT: A 616 ARG cc_start: 0.8547 (ptp-110) cc_final: 0.7860 (ptp-110) REVERT: B 54 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.7740 (t80) REVERT: B 395 LYS cc_start: 0.8265 (mmtm) cc_final: 0.7794 (mtmt) REVERT: B 616 ARG cc_start: 0.8548 (ptp-110) cc_final: 0.7860 (ptp-110) REVERT: C 145 ASP cc_start: 0.8013 (p0) cc_final: 0.7663 (p0) REVERT: C 447 ASP cc_start: 0.7890 (t70) cc_final: 0.7505 (t0) REVERT: C 485 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8669 (ttp-170) REVERT: C 674 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.7121 (mm-40) REVERT: D 145 ASP cc_start: 0.8019 (p0) cc_final: 0.7658 (p0) REVERT: D 447 ASP cc_start: 0.7891 (t70) cc_final: 0.7508 (t0) REVERT: D 485 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8656 (ttp-170) REVERT: D 674 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.7117 (mm-40) outliers start: 62 outliers final: 56 residues processed: 221 average time/residue: 0.1626 time to fit residues: 55.3205 Evaluate side-chains 235 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 173 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 266 ARG Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 297 PHE Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 485 ARG Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 674 GLN Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 266 ARG Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 297 PHE Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 485 ARG Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 674 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 148 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 75 optimal weight: 0.0570 chunk 108 optimal weight: 0.5980 chunk 185 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 251 optimal weight: 0.6980 chunk 165 optimal weight: 4.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.127423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.106320 restraints weight = 28043.778| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.07 r_work: 0.3150 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21428 Z= 0.099 Angle : 0.432 7.548 28984 Z= 0.229 Chirality : 0.041 0.157 3208 Planarity : 0.003 0.025 3708 Dihedral : 7.827 71.049 2996 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.45 % Allowed : 20.67 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.17), residues: 2488 helix: 2.40 (0.16), residues: 1016 sheet: 0.12 (0.23), residues: 508 loop : 0.36 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 74 TYR 0.007 0.001 TYR D 264 PHE 0.026 0.001 PHE B 439 TRP 0.006 0.001 TRP A 613 HIS 0.003 0.000 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00224 (21428) covalent geometry : angle 0.43217 (28984) hydrogen bonds : bond 0.02859 ( 992) hydrogen bonds : angle 4.15252 ( 2868) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4976 Ramachandran restraints generated. 2488 Oldfield, 0 Emsley, 2488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 187 time to evaluate : 0.827 Fit side-chains REVERT: A 54 PHE cc_start: 0.8580 (OUTLIER) cc_final: 0.7832 (t80) REVERT: A 395 LYS cc_start: 0.8236 (mmtm) cc_final: 0.7828 (mtmt) REVERT: A 517 MET cc_start: 0.8332 (mtp) cc_final: 0.7974 (mtt) REVERT: A 616 ARG cc_start: 0.8587 (ptp-110) cc_final: 0.7912 (ptp-110) REVERT: B 54 PHE cc_start: 0.8576 (OUTLIER) cc_final: 0.7817 (t80) REVERT: B 395 LYS cc_start: 0.8251 (mmtm) cc_final: 0.7836 (mtmt) REVERT: B 517 MET cc_start: 0.8330 (mtp) cc_final: 0.7968 (mtt) REVERT: B 616 ARG cc_start: 0.8588 (ptp-110) cc_final: 0.7910 (ptp-110) REVERT: C 145 ASP cc_start: 0.7992 (p0) cc_final: 0.7648 (p0) REVERT: C 266 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8172 (mtp85) REVERT: C 447 ASP cc_start: 0.7855 (t70) cc_final: 0.7539 (t0) REVERT: C 674 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.7046 (mm-40) REVERT: D 145 ASP cc_start: 0.7998 (p0) cc_final: 0.7644 (p0) REVERT: D 266 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8155 (mtp85) REVERT: D 447 ASP cc_start: 0.7861 (t70) cc_final: 0.7545 (t0) REVERT: D 674 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.7025 (mm-40) outliers start: 56 outliers final: 44 residues processed: 223 average time/residue: 0.1609 time to fit residues: 55.1637 Evaluate side-chains 228 residues out of total 2284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 178 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 266 ARG Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 297 PHE Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 674 GLN Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 266 ARG Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 297 PHE Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 674 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 59 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 189 optimal weight: 7.9990 chunk 246 optimal weight: 0.8980 chunk 87 optimal weight: 9.9990 chunk 192 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN A 509 ASN B 310 ASN B 509 ASN D 539 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.125117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.103909 restraints weight = 28171.055| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.07 r_work: 0.3115 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21428 Z= 0.154 Angle : 0.473 7.368 28984 Z= 0.247 Chirality : 0.042 0.159 3208 Planarity : 0.003 0.027 3708 Dihedral : 7.920 72.230 2996 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.71 % Allowed : 20.40 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.17), residues: 2488 helix: 2.26 (0.16), residues: 1016 sheet: 0.08 (0.23), residues: 508 loop : 0.28 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 74 TYR 0.008 0.001 TYR B 130 PHE 0.030 0.001 PHE B 439 TRP 0.005 0.001 TRP D 613 HIS 0.004 0.001 HIS B 454 Details of bonding type rmsd covalent geometry : bond 0.00371 (21428) covalent geometry : angle 0.47281 (28984) hydrogen bonds : bond 0.03317 ( 992) hydrogen bonds : angle 4.27734 ( 2868) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4742.61 seconds wall clock time: 82 minutes 8.92 seconds (4928.92 seconds total)