Starting phenix.real_space_refine on Thu Aug 6 14:12:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vxp_65437/08_2026/9vxp_65437.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vxp_65437/08_2026/9vxp_65437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vxp_65437/08_2026/9vxp_65437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vxp_65437/08_2026/9vxp_65437.map" model { file = "/net/cci-nas-00/data/ceres_data/9vxp_65437/08_2026/9vxp_65437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vxp_65437/08_2026/9vxp_65437.cif" } resolution = 2.48 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= 0.003 sd= 0.039 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: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 9644 2.51 5 N 2780 2.21 5 O 2856 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15348 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3837 Classifications: {'peptide': 507} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 481} Chain: "B" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3837 Classifications: {'peptide': 507} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 481} Chain: "C" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3837 Classifications: {'peptide': 507} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 481} Chain: "D" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3837 Classifications: {'peptide': 507} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 481} Time building chain proxies: 3.43, per 1000 atoms: 0.22 Number of scatterers: 15348 At special positions: 0 Unit cell: (97.75, 153.85, 114.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 2856 8.00 N 2780 7.00 C 9644 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: 1.26 Conformation dependent library (CDL) restraints added in 667.4 milliseconds 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 10 sheets defined 43.7% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.944A pdb=" N LEU A 73 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 111 Processing helix chain 'A' and resid 123 through 140 removed outlier: 3.530A pdb=" N HIS A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 148 Processing helix chain 'A' and resid 204 through 210 removed outlier: 4.272A pdb=" N VAL A 208 " --> pdb=" O PRO A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 279 removed outlier: 4.112A pdb=" N ARG A 270 " --> pdb=" O GLU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 302 removed outlier: 3.799A pdb=" N VAL A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY A 302 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 322 Processing helix chain 'A' and resid 322 through 330 Processing helix chain 'A' and resid 348 through 364 Processing helix chain 'A' and resid 375 through 379 Processing helix chain 'A' and resid 384 through 398 removed outlier: 3.974A pdb=" N GLY A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 431 removed outlier: 3.738A pdb=" N ALA A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 445 Processing helix chain 'A' and resid 450 through 467 removed outlier: 3.550A pdb=" N VAL A 454 " --> pdb=" O ASP A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 487 removed outlier: 4.108A pdb=" N TYR A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 506 Processing helix chain 'A' and resid 507 through 509 No H-bonds generated for 'chain 'A' and resid 507 through 509' Processing helix chain 'A' and resid 524 through 543 Processing helix chain 'B' and resid 70 through 74 removed outlier: 4.019A pdb=" N LEU B 73 " --> pdb=" O LEU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 111 Processing helix chain 'B' and resid 123 through 140 removed outlier: 3.516A pdb=" N HIS B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 148 removed outlier: 3.500A pdb=" N TYR B 148 " --> pdb=" O PRO B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 210 removed outlier: 4.192A pdb=" N VAL B 208 " --> pdb=" O PRO B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 279 removed outlier: 4.165A pdb=" N ARG B 270 " --> pdb=" O GLU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 302 removed outlier: 3.755A pdb=" N VAL B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY B 302 " --> pdb=" O ARG B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 322 Processing helix chain 'B' and resid 322 through 330 Processing helix chain 'B' and resid 348 through 364 Processing helix chain 'B' and resid 375 through 379 Processing helix chain 'B' and resid 384 through 398 removed outlier: 3.549A pdb=" N THR B 388 " --> pdb=" O THR B 384 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.902A pdb=" N ALA B 409 " --> pdb=" O SER B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 431 removed outlier: 3.700A pdb=" N ALA B 431 " --> pdb=" O GLU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 445 Processing helix chain 'B' and resid 450 through 467 removed outlier: 3.522A pdb=" N VAL B 454 " --> pdb=" O ASP B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 487 removed outlier: 4.000A pdb=" N TYR B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 506 Processing helix chain 'B' and resid 507 through 509 No H-bonds generated for 'chain 'B' and resid 507 through 509' Processing helix chain 'B' and resid 524 through 543 Processing helix chain 'C' and resid 70 through 74 removed outlier: 4.085A pdb=" N LEU C 73 " --> pdb=" O LEU C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 111 Processing helix chain 'C' and resid 123 through 140 removed outlier: 3.545A pdb=" N HIS C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 148 Processing helix chain 'C' and resid 204 through 210 removed outlier: 4.226A pdb=" N VAL C 208 " --> pdb=" O PRO C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 279 removed outlier: 4.202A pdb=" N ARG C 270 " --> pdb=" O GLU C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 302 removed outlier: 3.759A pdb=" N VAL C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 322 Processing helix chain 'C' and resid 322 through 330 Processing helix chain 'C' and resid 345 through 347 No H-bonds generated for 'chain 'C' and resid 345 through 347' Processing helix chain 'C' and resid 348 through 364 Processing helix chain 'C' and resid 375 through 379 Processing helix chain 'C' and resid 384 through 398 removed outlier: 3.517A pdb=" N THR C 388 " --> pdb=" O THR C 384 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY C 398 " --> pdb=" O ALA C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.804A pdb=" N ALA C 409 " --> pdb=" O SER C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 431 removed outlier: 3.799A pdb=" N ALA C 431 " --> pdb=" O GLU C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 445 Processing helix chain 'C' and resid 450 through 467 removed outlier: 3.524A pdb=" N VAL C 454 " --> pdb=" O ASP C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 487 removed outlier: 4.066A pdb=" N TYR C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 506 Processing helix chain 'C' and resid 507 through 509 No H-bonds generated for 'chain 'C' and resid 507 through 509' Processing helix chain 'C' and resid 524 through 543 Processing helix chain 'D' and resid 70 through 74 removed outlier: 3.998A pdb=" N LEU D 73 " --> pdb=" O LEU D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 111 Processing helix chain 'D' and resid 123 through 140 Processing helix chain 'D' and resid 144 through 148 Processing helix chain 'D' and resid 204 through 210 removed outlier: 4.241A pdb=" N VAL D 208 " --> pdb=" O PRO D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 279 removed outlier: 4.165A pdb=" N ARG D 270 " --> pdb=" O GLU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 302 removed outlier: 3.775A pdb=" N VAL D 294 " --> pdb=" O LYS D 290 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY D 302 " --> pdb=" O ARG D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 322 Processing helix chain 'D' and resid 322 through 330 Processing helix chain 'D' and resid 345 through 347 No H-bonds generated for 'chain 'D' and resid 345 through 347' Processing helix chain 'D' and resid 348 through 364 Processing helix chain 'D' and resid 374 through 379 removed outlier: 3.557A pdb=" N MET D 377 " --> pdb=" O LEU D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 398 removed outlier: 3.512A pdb=" N THR D 388 " --> pdb=" O THR D 384 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY D 398 " --> pdb=" O ALA D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 431 removed outlier: 3.735A pdb=" N ALA D 431 " --> pdb=" O GLU D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 445 Processing helix chain 'D' and resid 450 through 467 Processing helix chain 'D' and resid 478 through 487 removed outlier: 4.057A pdb=" N TYR D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 506 Processing helix chain 'D' and resid 507 through 509 No H-bonds generated for 'chain 'D' and resid 507 through 509' Processing helix chain 'D' and resid 524 through 543 removed outlier: 3.506A pdb=" N ASP D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 93 removed outlier: 6.665A pdb=" N ILE A 90 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ARG A 116 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA A 92 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N ASN A 118 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA A 115 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ASP A 156 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU A 117 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE A 153 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N PHE A 284 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU A 155 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY A 332 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS A 401 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET A 403 " --> pdb=" O CYS A 369 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 201 removed outlier: 7.892A pdb=" N VAL A 200 " --> pdb=" O GLN A 182 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LEU A 184 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL A 237 " --> pdb=" O GLN A 229 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 512 through 516 removed outlier: 6.996A pdb=" N VAL A 493 " --> pdb=" O PHE A 513 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU A 515 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA A 495 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE A 471 " --> pdb=" O ILE A 494 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL A 496 " --> pdb=" O ILE A 471 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL A 473 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA A 470 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR A 556 " --> pdb=" O ILE A 567 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 567 " --> pdb=" O THR A 556 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE B 567 " --> pdb=" O THR B 556 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR B 556 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA B 470 " --> pdb=" O LEU B 551 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE B 471 " --> pdb=" O ILE B 494 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL B 496 " --> pdb=" O ILE B 471 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL B 473 " --> pdb=" O VAL B 496 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL B 493 " --> pdb=" O PHE B 513 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LEU B 515 " --> pdb=" O VAL B 493 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA B 495 " --> pdb=" O LEU B 515 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 89 through 93 removed outlier: 6.745A pdb=" N ILE B 90 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ARG B 116 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA B 92 " --> pdb=" O ARG B 116 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ASN B 118 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA B 115 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ASP B 156 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU B 117 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE B 153 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N PHE B 284 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU B 155 " --> pdb=" O PHE B 284 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY B 332 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS B 401 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET B 403 " --> pdb=" O CYS B 369 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 199 through 201 removed outlier: 7.883A pdb=" N VAL B 200 " --> pdb=" O GLN B 182 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU B 184 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL B 237 " --> pdb=" O GLN B 229 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 89 through 93 removed outlier: 6.714A pdb=" N ILE C 90 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ARG C 116 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA C 92 " --> pdb=" O ARG C 116 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ASN C 118 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA C 115 " --> pdb=" O ALA C 154 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ASP C 156 " --> pdb=" O ALA C 115 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU C 117 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE C 153 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N PHE C 284 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU C 155 " --> pdb=" O PHE C 284 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY C 332 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS C 401 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET C 403 " --> pdb=" O CYS C 369 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 199 through 201 removed outlier: 7.823A pdb=" N VAL C 200 " --> pdb=" O GLN C 182 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU C 184 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL C 237 " --> pdb=" O GLN C 229 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 512 through 516 removed outlier: 6.990A pdb=" N VAL C 493 " --> pdb=" O PHE C 513 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU C 515 " --> pdb=" O VAL C 493 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA C 495 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE C 471 " --> pdb=" O ILE C 494 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL C 496 " --> pdb=" O ILE C 471 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL C 473 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA C 470 " --> pdb=" O LEU C 551 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR C 556 " --> pdb=" O ILE C 567 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE C 567 " --> pdb=" O THR C 556 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA D 470 " --> pdb=" O LEU D 551 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE D 471 " --> pdb=" O ILE D 494 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL D 496 " --> pdb=" O ILE D 471 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL D 473 " --> pdb=" O VAL D 496 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL D 493 " --> pdb=" O PHE D 513 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU D 515 " --> pdb=" O VAL D 493 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA D 495 " --> pdb=" O LEU D 515 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 89 through 93 removed outlier: 6.681A pdb=" N ILE D 90 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ARG D 116 " --> pdb=" O ILE D 90 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA D 92 " --> pdb=" O ARG D 116 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ASN D 118 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA D 115 " --> pdb=" O ALA D 154 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ASP D 156 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU D 117 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE D 153 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N PHE D 284 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU D 155 " --> pdb=" O PHE D 284 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N MET D 334 " --> pdb=" O ILE D 310 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N SER D 312 " --> pdb=" O MET D 334 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS D 401 " --> pdb=" O VAL D 367 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET D 403 " --> pdb=" O CYS D 369 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 199 through 201 removed outlier: 7.773A pdb=" N VAL D 200 " --> pdb=" O GLN D 182 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU D 184 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLY D 235 " --> pdb=" O ILE D 231 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE D 231 " --> pdb=" O GLY D 235 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL D 237 " --> pdb=" O GLN D 229 " (cutoff:3.500A) 682 hydrogen bonds defined for protein. 1932 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5295 1.34 - 1.46: 3042 1.46 - 1.58: 7155 1.58 - 1.70: 0 1.70 - 1.82: 108 Bond restraints: 15600 Sorted by residual: bond pdb=" N MET D 355 " pdb=" CA MET D 355 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.28e-02 6.10e+03 5.59e+00 bond pdb=" N PHE C 191 " pdb=" CA PHE C 191 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.24e-02 6.50e+03 3.42e+00 bond pdb=" CB GLU A 375 " pdb=" CG GLU A 375 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.19e+00 bond pdb=" CB GLU B 277 " pdb=" CG GLU B 277 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.64e+00 bond pdb=" CB LYS C 410 " pdb=" CG LYS C 410 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.40e+00 ... (remaining 15595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 20537 1.38 - 2.75: 373 2.75 - 4.13: 176 4.13 - 5.50: 51 5.50 - 6.88: 11 Bond angle restraints: 21148 Sorted by residual: angle pdb=" CA MET D 355 " pdb=" C MET D 355 " pdb=" O MET D 355 " ideal model delta sigma weight residual 119.97 115.58 4.39 1.15e+00 7.56e-01 1.46e+01 angle pdb=" CA PHE C 191 " pdb=" C PHE C 191 " pdb=" O PHE C 191 " ideal model delta sigma weight residual 120.60 116.60 4.00 1.13e+00 7.83e-01 1.26e+01 angle pdb=" CB GLU A 375 " pdb=" CG GLU A 375 " pdb=" CD GLU A 375 " ideal model delta sigma weight residual 112.60 117.93 -5.33 1.70e+00 3.46e-01 9.81e+00 angle pdb=" CA GLU B 277 " pdb=" CB GLU B 277 " pdb=" CG GLU B 277 " ideal model delta sigma weight residual 114.10 120.03 -5.93 2.00e+00 2.50e-01 8.80e+00 angle pdb=" CA GLU A 375 " pdb=" CB GLU A 375 " pdb=" CG GLU A 375 " ideal model delta sigma weight residual 114.10 119.90 -5.80 2.00e+00 2.50e-01 8.41e+00 ... (remaining 21143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 8089 17.19 - 34.39: 1000 34.39 - 51.58: 331 51.58 - 68.78: 63 68.78 - 85.97: 33 Dihedral angle restraints: 9516 sinusoidal: 3764 harmonic: 5752 Sorted by residual: dihedral pdb=" CG ARG A 486 " pdb=" CD ARG A 486 " pdb=" NE ARG A 486 " pdb=" CZ ARG A 486 " ideal model delta sinusoidal sigma weight residual -90.00 -40.26 -49.74 2 1.50e+01 4.44e-03 1.24e+01 dihedral pdb=" CG ARG D 426 " pdb=" CD ARG D 426 " pdb=" NE ARG D 426 " pdb=" CZ ARG D 426 " ideal model delta sinusoidal sigma weight residual 90.00 41.44 48.56 2 1.50e+01 4.44e-03 1.20e+01 dihedral pdb=" CG ARG C 426 " pdb=" CD ARG C 426 " pdb=" NE ARG C 426 " pdb=" CZ ARG C 426 " ideal model delta sinusoidal sigma weight residual 90.00 41.44 48.56 2 1.50e+01 4.44e-03 1.20e+01 ... (remaining 9513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1516 0.029 - 0.059: 549 0.059 - 0.088: 161 0.088 - 0.118: 178 0.118 - 0.147: 60 Chirality restraints: 2464 Sorted by residual: chirality pdb=" CA ILE A 344 " pdb=" N ILE A 344 " pdb=" C ILE A 344 " pdb=" CB ILE A 344 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CA ILE C 344 " pdb=" N ILE C 344 " pdb=" C ILE C 344 " pdb=" CB ILE C 344 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA ILE B 344 " pdb=" N ILE B 344 " pdb=" C ILE B 344 " pdb=" CB ILE B 344 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 2461 not shown) Planarity restraints: 2776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 486 " 0.261 9.50e-02 1.11e+02 1.17e-01 9.25e+00 pdb=" NE ARG A 486 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 486 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 486 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 486 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 426 " -0.254 9.50e-02 1.11e+02 1.14e-01 8.82e+00 pdb=" NE ARG C 426 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG C 426 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG C 426 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG C 426 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 426 " 0.254 9.50e-02 1.11e+02 1.14e-01 8.79e+00 pdb=" NE ARG D 426 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG D 426 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG D 426 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG D 426 " 0.004 2.00e-02 2.50e+03 ... (remaining 2773 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 156 2.66 - 3.22: 13442 3.22 - 3.78: 21935 3.78 - 4.34: 28747 4.34 - 4.90: 49892 Nonbonded interactions: 114172 Sorted by model distance: nonbonded pdb=" OG SER B 87 " pdb=" OE1 GLU B 429 " model vdw 2.097 3.040 nonbonded pdb=" OG SER C 87 " pdb=" OE2 GLU C 429 " model vdw 2.129 3.040 nonbonded pdb=" OG SER B 100 " pdb=" OE1 GLU B 102 " model vdw 2.205 3.040 nonbonded pdb=" OG SER D 100 " pdb=" OE1 GLU D 102 " model vdw 2.229 3.040 nonbonded pdb=" OE1 GLU B 277 " pdb=" ND1 HIS B 278 " model vdw 2.247 3.120 ... (remaining 114167 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.620 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15600 Z= 0.126 Angle : 0.590 6.875 21148 Z= 0.294 Chirality : 0.045 0.147 2464 Planarity : 0.007 0.117 2776 Dihedral : 17.609 85.969 5820 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 24.45 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.20), residues: 2020 helix: 2.74 (0.19), residues: 804 sheet: 1.33 (0.25), residues: 416 loop : -0.62 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 426 TYR 0.008 0.001 TYR D 126 PHE 0.009 0.001 PHE C 191 TRP 0.006 0.001 TRP D 525 HIS 0.008 0.001 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (15600) covalent geometry : angle 0.59027 / 0.29 (21148) hydrogen bonds : bond 0.17696 / 11.94 ( 682) hydrogen bonds : angle 4.87726 / 3.50 ( 1932) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 397 time to evaluate : 0.548 Fit side-chains REVERT: A 250 LYS cc_start: 0.6953 (mtpt) cc_final: 0.6732 (mtpt) REVERT: A 407 GLU cc_start: 0.8137 (mp0) cc_final: 0.7712 (mp0) REVERT: B 221 ASP cc_start: 0.7915 (t0) cc_final: 0.7697 (t0) REVERT: B 407 GLU cc_start: 0.7906 (mp0) cc_final: 0.7369 (pm20) REVERT: C 250 LYS cc_start: 0.7018 (mtpt) cc_final: 0.6733 (mtpt) REVERT: D 221 ASP cc_start: 0.7920 (t0) cc_final: 0.7708 (t0) REVERT: D 250 LYS cc_start: 0.7054 (mtpt) cc_final: 0.6718 (mtpt) REVERT: D 407 GLU cc_start: 0.8020 (mp0) cc_final: 0.7738 (mp0) outliers start: 0 outliers final: 1 residues processed: 397 average time/residue: 0.7532 time to fit residues: 322.0666 Evaluate side-chains 386 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 385 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN A 133 ASN A 168 GLN A 306 HIS A 421 GLN B 421 GLN C 118 ASN C 133 ASN C 253 ASN C 306 HIS C 412 ASN C 421 GLN D 118 ASN D 306 HIS D 353 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.162430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.133545 restraints weight = 19991.429| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.09 r_work: 0.3633 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15600 Z= 0.198 Angle : 0.572 8.092 21148 Z= 0.299 Chirality : 0.048 0.162 2464 Planarity : 0.005 0.044 2776 Dihedral : 3.596 18.092 2222 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.98 % Allowed : 20.39 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.19), residues: 2020 helix: 2.45 (0.18), residues: 812 sheet: 1.05 (0.25), residues: 424 loop : -0.80 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 486 TYR 0.012 0.002 TYR B 126 PHE 0.015 0.002 PHE C 284 TRP 0.007 0.002 TRP D 558 HIS 0.006 0.002 HIS C 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.20 (15600) covalent geometry : angle 0.57204 / 0.30 (21148) hydrogen bonds : bond 0.06756 / 4.63 ( 682) hydrogen bonds : angle 3.63393 / 2.59 ( 1932) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 367 time to evaluate : 0.622 Fit side-chains REVERT: A 168 GLN cc_start: 0.1049 (OUTLIER) cc_final: 0.0659 (mt0) REVERT: A 191 PHE cc_start: 0.7626 (OUTLIER) cc_final: 0.7196 (t80) REVERT: A 250 LYS cc_start: 0.7298 (OUTLIER) cc_final: 0.6976 (mtpt) REVERT: A 407 GLU cc_start: 0.8207 (mp0) cc_final: 0.7966 (mp0) REVERT: B 362 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8422 (mp) REVERT: B 373 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.7026 (mmt) REVERT: B 387 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7594 (mt-10) REVERT: B 407 GLU cc_start: 0.8118 (mp0) cc_final: 0.7301 (pm20) REVERT: B 522 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7066 (mt-10) REVERT: C 250 LYS cc_start: 0.7295 (mtpt) cc_final: 0.6972 (mtpt) REVERT: C 375 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7687 (tm-30) REVERT: C 427 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7727 (mp0) REVERT: C 461 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7395 (tm-30) REVERT: D 191 PHE cc_start: 0.7686 (OUTLIER) cc_final: 0.7214 (t80) REVERT: D 250 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.7130 (mtpt) REVERT: D 427 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7672 (mp0) outliers start: 81 outliers final: 41 residues processed: 403 average time/residue: 0.6917 time to fit residues: 301.2566 Evaluate side-chains 409 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 358 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 466 CYS Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 538 GLU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 353 GLN Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 466 CYS Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain D residue 121 HIS Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 292 SER Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 538 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 6 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 112 optimal weight: 0.2980 chunk 136 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 GLN B 168 GLN B 421 GLN C 118 ASN C 133 ASN C 168 GLN C 412 ASN C 421 GLN D 168 GLN D 253 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.160751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.131898 restraints weight = 19952.242| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.11 r_work: 0.3612 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 15600 Z= 0.271 Angle : 0.625 9.491 21148 Z= 0.328 Chirality : 0.050 0.172 2464 Planarity : 0.005 0.041 2776 Dihedral : 4.048 19.273 2222 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 7.06 % Allowed : 19.78 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.19), residues: 2020 helix: 1.98 (0.18), residues: 812 sheet: 0.83 (0.25), residues: 416 loop : -1.02 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 426 TYR 0.013 0.002 TYR B 126 PHE 0.019 0.002 PHE D 284 TRP 0.011 0.002 TRP D 525 HIS 0.007 0.002 HIS D 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00690 / 0.27 (15600) covalent geometry : angle 0.62492 / 0.33 (21148) hydrogen bonds : bond 0.07906 / 5.42 ( 682) hydrogen bonds : angle 3.71340 / 2.65 ( 1932) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 397 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7928 (mpt-90) REVERT: A 144 SER cc_start: 0.8403 (OUTLIER) cc_final: 0.8202 (p) REVERT: A 191 PHE cc_start: 0.7679 (OUTLIER) cc_final: 0.7161 (t80) REVERT: A 250 LYS cc_start: 0.7549 (mtpt) cc_final: 0.7202 (mtpt) REVERT: A 407 GLU cc_start: 0.8159 (mp0) cc_final: 0.7853 (mp0) REVERT: B 168 GLN cc_start: 0.1827 (OUTLIER) cc_final: 0.1538 (mt0) REVERT: B 267 GLN cc_start: 0.8375 (tp40) cc_final: 0.8102 (tp40) REVERT: B 439 GLU cc_start: 0.6370 (OUTLIER) cc_final: 0.5625 (mp0) REVERT: C 103 ARG cc_start: 0.8490 (mmt90) cc_final: 0.8277 (tpt-90) REVERT: C 168 GLN cc_start: 0.2711 (OUTLIER) cc_final: 0.2067 (mt0) REVERT: C 267 GLN cc_start: 0.8394 (tp40) cc_final: 0.8110 (tp40) REVERT: C 427 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7772 (mp0) REVERT: D 168 GLN cc_start: 0.2291 (OUTLIER) cc_final: 0.1814 (mt0) REVERT: D 191 PHE cc_start: 0.7755 (OUTLIER) cc_final: 0.7277 (t80) REVERT: D 250 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7200 (mtpt) REVERT: D 373 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.7212 (mmt) REVERT: D 390 ASP cc_start: 0.8097 (t0) cc_final: 0.7551 (t70) REVERT: D 427 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7725 (mp0) outliers start: 115 outliers final: 66 residues processed: 447 average time/residue: 0.7692 time to fit residues: 371.0086 Evaluate side-chains 469 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 391 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 466 CYS Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 230 LYS Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 466 CYS Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain D residue 121 HIS Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 168 GLN Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 292 SER Chi-restraints excluded: chain D residue 373 MET Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 488 ARG Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 548 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 62 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 186 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 GLN A 421 GLN B 421 GLN C 133 ASN C 412 ASN C 421 GLN D 421 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.162810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.134206 restraints weight = 19961.630| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.09 r_work: 0.3635 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15600 Z= 0.147 Angle : 0.544 9.447 21148 Z= 0.281 Chirality : 0.046 0.155 2464 Planarity : 0.005 0.041 2776 Dihedral : 3.804 20.128 2222 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 5.28 % Allowed : 22.48 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.19), residues: 2020 helix: 2.17 (0.18), residues: 812 sheet: 0.75 (0.25), residues: 424 loop : -1.00 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 426 TYR 0.011 0.001 TYR A 126 PHE 0.012 0.001 PHE C 274 TRP 0.011 0.001 TRP D 525 HIS 0.004 0.001 HIS C 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (15600) covalent geometry : angle 0.54359 / 0.28 (21148) hydrogen bonds : bond 0.05601 / 3.85 ( 682) hydrogen bonds : angle 3.45836 / 2.47 ( 1932) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 393 time to evaluate : 0.630 Fit side-chains REVERT: A 103 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7854 (mpt-90) REVERT: A 191 PHE cc_start: 0.7612 (OUTLIER) cc_final: 0.7099 (t80) REVERT: A 250 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.7082 (mtpt) REVERT: A 387 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7754 (mt-10) REVERT: A 407 GLU cc_start: 0.8134 (mp0) cc_final: 0.7573 (mp0) REVERT: B 267 GLN cc_start: 0.8358 (tp40) cc_final: 0.8102 (tp40) REVERT: B 270 ARG cc_start: 0.8239 (mtm-85) cc_final: 0.8025 (mtm110) REVERT: B 373 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7060 (mmt) REVERT: B 387 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7506 (mt-10) REVERT: B 407 GLU cc_start: 0.8103 (mp0) cc_final: 0.7419 (pm20) REVERT: B 439 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.5860 (mp0) REVERT: C 250 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.7064 (mtpt) REVERT: C 267 GLN cc_start: 0.8363 (tp40) cc_final: 0.8119 (tp40) REVERT: C 407 GLU cc_start: 0.8187 (mp0) cc_final: 0.7917 (mp0) REVERT: C 427 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7640 (mp0) REVERT: D 250 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7109 (mtpt) REVERT: D 276 VAL cc_start: 0.8797 (OUTLIER) cc_final: 0.8521 (t) REVERT: D 373 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.7406 (mmt) REVERT: D 407 GLU cc_start: 0.8065 (mp0) cc_final: 0.7645 (mp0) outliers start: 86 outliers final: 53 residues processed: 428 average time/residue: 0.7457 time to fit residues: 343.8907 Evaluate side-chains 454 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 390 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 466 CYS Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain C residue 230 LYS Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 466 CYS Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain D residue 121 HIS Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain D residue 373 MET Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 501 GLN Chi-restraints excluded: chain D residue 506 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 178 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 171 optimal weight: 4.9990 chunk 189 optimal weight: 2.9990 chunk 173 optimal weight: 0.0370 chunk 30 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 GLN A 421 GLN B 168 GLN B 306 HIS B 421 GLN B 534 GLN C 133 ASN C 412 ASN C 421 GLN D 168 GLN D 421 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.162227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.133692 restraints weight = 19909.616| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.09 r_work: 0.3642 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15600 Z= 0.165 Angle : 0.547 9.636 21148 Z= 0.282 Chirality : 0.047 0.158 2464 Planarity : 0.005 0.047 2776 Dihedral : 3.774 17.999 2222 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 6.02 % Allowed : 22.17 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.19), residues: 2020 helix: 2.17 (0.18), residues: 812 sheet: 0.71 (0.25), residues: 424 loop : -1.05 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 486 TYR 0.011 0.001 TYR A 126 PHE 0.013 0.002 PHE C 274 TRP 0.011 0.001 TRP D 525 HIS 0.005 0.001 HIS C 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.16 (15600) covalent geometry : angle 0.54669 / 0.28 (21148) hydrogen bonds : bond 0.05957 / 4.10 ( 682) hydrogen bonds : angle 3.46050 / 2.47 ( 1932) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 397 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7911 (mpt-90) REVERT: A 191 PHE cc_start: 0.7614 (OUTLIER) cc_final: 0.7081 (t80) REVERT: A 250 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.7104 (mtpt) REVERT: A 387 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7734 (mt-10) REVERT: A 407 GLU cc_start: 0.8111 (mp0) cc_final: 0.7535 (mp0) REVERT: B 168 GLN cc_start: 0.1472 (OUTLIER) cc_final: 0.1230 (mt0) REVERT: B 267 GLN cc_start: 0.8369 (tp40) cc_final: 0.8109 (tp40) REVERT: B 270 ARG cc_start: 0.8263 (mtm-85) cc_final: 0.8062 (mtm110) REVERT: B 373 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.7165 (mmt) REVERT: B 387 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7492 (mt-10) REVERT: B 407 GLU cc_start: 0.8118 (mp0) cc_final: 0.7440 (pm20) REVERT: B 439 GLU cc_start: 0.6347 (OUTLIER) cc_final: 0.5717 (mp0) REVERT: B 522 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.7057 (mt-10) REVERT: C 216 ARG cc_start: 0.8092 (tpp80) cc_final: 0.7795 (tpp80) REVERT: C 267 GLN cc_start: 0.8379 (tp40) cc_final: 0.8140 (tp40) REVERT: C 407 GLU cc_start: 0.8177 (mp0) cc_final: 0.7864 (mp0) REVERT: C 427 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7728 (mp0) REVERT: D 168 GLN cc_start: 0.1868 (OUTLIER) cc_final: 0.1541 (mt0) REVERT: D 250 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7129 (mtpt) REVERT: D 373 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.7421 (mmt) REVERT: D 427 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7578 (mp0) outliers start: 98 outliers final: 64 residues processed: 440 average time/residue: 0.7927 time to fit residues: 376.3437 Evaluate side-chains 469 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 393 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 466 CYS Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain C residue 230 LYS Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 466 CYS Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain D residue 121 HIS Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 168 GLN Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 292 SER Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 373 MET Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 488 ARG Chi-restraints excluded: chain D residue 501 GLN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 548 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 105 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 125 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 166 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 180 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 GLN B 421 GLN B 534 GLN C 133 ASN C 412 ASN C 421 GLN D 421 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.163743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.135451 restraints weight = 20026.973| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.08 r_work: 0.3634 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15600 Z= 0.132 Angle : 0.531 9.659 21148 Z= 0.270 Chirality : 0.046 0.151 2464 Planarity : 0.005 0.047 2776 Dihedral : 3.705 19.659 2222 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 5.96 % Allowed : 22.67 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.19), residues: 2020 helix: 2.28 (0.18), residues: 812 sheet: 0.72 (0.25), residues: 424 loop : -1.02 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 426 TYR 0.010 0.001 TYR A 126 PHE 0.013 0.001 PHE D 513 TRP 0.011 0.001 TRP D 525 HIS 0.004 0.001 HIS C 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (15600) covalent geometry : angle 0.53103 / 0.27 (21148) hydrogen bonds : bond 0.05158 / 3.55 ( 682) hydrogen bonds : angle 3.36738 / 2.41 ( 1932) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 398 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7872 (mpt-90) REVERT: A 191 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.7117 (t80) REVERT: A 250 LYS cc_start: 0.7459 (OUTLIER) cc_final: 0.7058 (mtpt) REVERT: A 387 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7732 (mt-10) REVERT: A 407 GLU cc_start: 0.8113 (mp0) cc_final: 0.7508 (mp0) REVERT: B 267 GLN cc_start: 0.8355 (tp40) cc_final: 0.8111 (tp40) REVERT: B 373 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.7076 (mmt) REVERT: B 387 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7487 (mt-10) REVERT: B 407 GLU cc_start: 0.8118 (mp0) cc_final: 0.7396 (pm20) REVERT: B 439 GLU cc_start: 0.6276 (OUTLIER) cc_final: 0.5637 (mp0) REVERT: B 522 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7095 (mt-10) REVERT: C 216 ARG cc_start: 0.8084 (tpp80) cc_final: 0.7785 (tpp80) REVERT: C 267 GLN cc_start: 0.8329 (tp40) cc_final: 0.8030 (tp40) REVERT: C 276 VAL cc_start: 0.8785 (t) cc_final: 0.8532 (t) REVERT: C 407 GLU cc_start: 0.8181 (mp0) cc_final: 0.7853 (mp0) REVERT: D 250 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7099 (mtpt) REVERT: D 276 VAL cc_start: 0.8782 (OUTLIER) cc_final: 0.8519 (t) REVERT: D 387 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7412 (mt-10) REVERT: D 407 GLU cc_start: 0.8066 (mp0) cc_final: 0.7741 (mp0) REVERT: D 427 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7544 (mp0) outliers start: 97 outliers final: 68 residues processed: 438 average time/residue: 0.7883 time to fit residues: 372.2366 Evaluate side-chains 474 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 396 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 466 CYS Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 230 LYS Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain D residue 121 HIS Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 488 ARG Chi-restraints excluded: chain D residue 501 GLN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 548 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 72 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 118 optimal weight: 0.0970 chunk 165 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 GLN B 168 GLN B 421 GLN C 133 ASN C 412 ASN C 421 GLN D 168 GLN D 421 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.161326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.133006 restraints weight = 19851.717| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.08 r_work: 0.3612 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15600 Z= 0.215 Angle : 0.591 9.738 21148 Z= 0.303 Chirality : 0.048 0.163 2464 Planarity : 0.005 0.041 2776 Dihedral : 3.942 18.545 2222 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 6.27 % Allowed : 23.34 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.19), residues: 2020 helix: 2.07 (0.18), residues: 812 sheet: 0.64 (0.25), residues: 424 loop : -1.14 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 426 TYR 0.012 0.002 TYR B 126 PHE 0.014 0.002 PHE C 274 TRP 0.010 0.002 TRP D 525 HIS 0.006 0.002 HIS D 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.21 (15600) covalent geometry : angle 0.59100 / 0.30 (21148) hydrogen bonds : bond 0.06846 / 4.71 ( 682) hydrogen bonds : angle 3.53720 / 2.53 ( 1932) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 397 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7909 (mpt-90) REVERT: A 191 PHE cc_start: 0.7684 (OUTLIER) cc_final: 0.7126 (t80) REVERT: A 250 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.7151 (mtpt) REVERT: A 322 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7614 (mmt-90) REVERT: A 375 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7624 (tm-30) REVERT: A 387 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7864 (mt-10) REVERT: A 407 GLU cc_start: 0.8109 (mp0) cc_final: 0.7553 (mp0) REVERT: B 315 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8294 (mt-10) REVERT: B 373 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.7186 (mmt) REVERT: B 387 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7355 (mt-10) REVERT: B 407 GLU cc_start: 0.8099 (mp0) cc_final: 0.7326 (pm20) REVERT: B 439 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.5747 (mp0) REVERT: C 276 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8613 (t) REVERT: D 168 GLN cc_start: 0.2150 (OUTLIER) cc_final: 0.1716 (mt0) REVERT: D 250 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7161 (mtpt) REVERT: D 427 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7671 (mp0) REVERT: D 545 PHE cc_start: 0.8239 (m-10) cc_final: 0.8022 (m-10) outliers start: 102 outliers final: 75 residues processed: 440 average time/residue: 0.7145 time to fit residues: 339.2788 Evaluate side-chains 476 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 390 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 292 SER Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 466 CYS Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain C residue 230 LYS Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 466 CYS Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain D residue 121 HIS Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 168 GLN Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 292 SER Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 427 GLU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 488 ARG Chi-restraints excluded: chain D residue 501 GLN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 548 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 171 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 chunk 188 optimal weight: 0.5980 chunk 141 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 181 optimal weight: 0.0870 overall best weight: 0.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 GLN B 421 GLN B 534 GLN C 133 ASN C 168 GLN C 412 ASN C 421 GLN D 168 GLN D 421 GLN D 436 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.164812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.136639 restraints weight = 20061.028| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.08 r_work: 0.3667 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15600 Z= 0.105 Angle : 0.517 9.526 21148 Z= 0.261 Chirality : 0.045 0.144 2464 Planarity : 0.004 0.044 2776 Dihedral : 3.623 17.989 2222 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.67 % Allowed : 25.86 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.19), residues: 2020 helix: 2.36 (0.19), residues: 812 sheet: 0.71 (0.25), residues: 424 loop : -1.01 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 382 TYR 0.010 0.001 TYR B 126 PHE 0.014 0.001 PHE D 513 TRP 0.014 0.001 TRP D 525 HIS 0.003 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 (15600) covalent geometry : angle 0.51712 / 0.26 (21148) hydrogen bonds : bond 0.04104 / 2.81 ( 682) hydrogen bonds : angle 3.29029 / 2.35 ( 1932) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 393 time to evaluate : 0.613 Fit side-chains REVERT: A 103 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7843 (mpt-90) REVERT: A 191 PHE cc_start: 0.7599 (OUTLIER) cc_final: 0.7068 (t80) REVERT: A 250 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.7041 (mtpt) REVERT: A 322 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7533 (mmt-90) REVERT: A 387 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7658 (mt-10) REVERT: A 407 GLU cc_start: 0.8108 (mp0) cc_final: 0.7649 (mp0) REVERT: A 522 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6900 (mt-10) REVERT: B 373 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7086 (mmt) REVERT: B 407 GLU cc_start: 0.8100 (mp0) cc_final: 0.7457 (pm20) REVERT: B 439 GLU cc_start: 0.6349 (OUTLIER) cc_final: 0.5713 (mp0) REVERT: B 522 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.7052 (mt-10) REVERT: C 168 GLN cc_start: 0.2822 (OUTLIER) cc_final: 0.2514 (mt0) REVERT: C 250 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.7037 (mtpt) REVERT: C 276 VAL cc_start: 0.8728 (OUTLIER) cc_final: 0.8475 (t) REVERT: C 407 GLU cc_start: 0.8182 (mp0) cc_final: 0.7816 (mp0) REVERT: D 168 GLN cc_start: 0.1693 (OUTLIER) cc_final: 0.0916 (mt0) REVERT: D 250 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.7090 (mtpt) REVERT: D 276 VAL cc_start: 0.8713 (t) cc_final: 0.8454 (t) REVERT: D 373 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.7328 (mtt) REVERT: D 387 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7327 (mt-10) REVERT: D 407 GLU cc_start: 0.8092 (mp0) cc_final: 0.7745 (mp0) outliers start: 76 outliers final: 45 residues processed: 426 average time/residue: 0.7449 time to fit residues: 342.6444 Evaluate side-chains 445 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 387 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 466 CYS Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain D residue 121 HIS Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 168 GLN Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 292 SER Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain D residue 373 MET Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 501 GLN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 548 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 182 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 99 optimal weight: 0.0970 chunk 57 optimal weight: 0.0770 chunk 55 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 199 optimal weight: 0.0020 overall best weight: 0.4344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 GLN B 421 GLN C 133 ASN C 168 GLN C 412 ASN C 421 GLN D 168 GLN D 421 GLN D 436 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.166235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.138272 restraints weight = 20041.209| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.07 r_work: 0.3689 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15600 Z= 0.090 Angle : 0.504 9.661 21148 Z= 0.251 Chirality : 0.045 0.139 2464 Planarity : 0.004 0.045 2776 Dihedral : 3.415 17.018 2220 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.62 % Allowed : 27.09 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.20), residues: 2020 helix: 2.52 (0.19), residues: 812 sheet: 0.76 (0.26), residues: 424 loop : -0.92 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 382 TYR 0.009 0.001 TYR B 126 PHE 0.015 0.001 PHE D 513 TRP 0.013 0.001 TRP D 525 HIS 0.003 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.09 (15600) covalent geometry : angle 0.50394 / 0.25 (21148) hydrogen bonds : bond 0.03606 / 2.48 ( 682) hydrogen bonds : angle 3.21180 / 2.29 ( 1932) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 380 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7805 (mpt-90) REVERT: A 191 PHE cc_start: 0.7596 (OUTLIER) cc_final: 0.7099 (t80) REVERT: A 250 LYS cc_start: 0.7294 (OUTLIER) cc_final: 0.6937 (mtpt) REVERT: A 375 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7473 (tm-30) REVERT: A 387 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7400 (mt-10) REVERT: A 407 GLU cc_start: 0.8062 (mp0) cc_final: 0.7188 (pm20) REVERT: B 373 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.6974 (mmt) REVERT: B 407 GLU cc_start: 0.8069 (mp0) cc_final: 0.7298 (pm20) REVERT: B 439 GLU cc_start: 0.6272 (OUTLIER) cc_final: 0.5622 (mp0) REVERT: C 276 VAL cc_start: 0.8678 (OUTLIER) cc_final: 0.8440 (t) REVERT: D 168 GLN cc_start: 0.1985 (OUTLIER) cc_final: 0.1627 (mt0) REVERT: D 250 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7027 (mtpt) REVERT: D 276 VAL cc_start: 0.8712 (t) cc_final: 0.8462 (t) outliers start: 59 outliers final: 40 residues processed: 412 average time/residue: 0.7875 time to fit residues: 349.6074 Evaluate side-chains 425 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 377 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 129 GLU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain D residue 121 HIS Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 168 GLN Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 501 GLN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 548 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 155 optimal weight: 0.0060 chunk 196 optimal weight: 0.9980 chunk 111 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 11 optimal weight: 0.0670 chunk 18 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 overall best weight: 0.5734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 GLN B 421 GLN C 133 ASN C 421 GLN D 168 GLN D 421 GLN D 436 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.166640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.138704 restraints weight = 20111.094| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.07 r_work: 0.3689 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15600 Z= 0.094 Angle : 0.501 9.365 21148 Z= 0.250 Chirality : 0.045 0.138 2464 Planarity : 0.004 0.043 2776 Dihedral : 3.343 16.545 2220 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.19 % Allowed : 27.27 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.20), residues: 2020 helix: 2.56 (0.19), residues: 812 sheet: 0.73 (0.25), residues: 464 loop : -0.77 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 426 TYR 0.010 0.001 TYR B 126 PHE 0.015 0.001 PHE D 513 TRP 0.011 0.001 TRP D 525 HIS 0.003 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.09 (15600) covalent geometry : angle 0.50113 / 0.25 (21148) hydrogen bonds : bond 0.03768 / 2.59 ( 682) hydrogen bonds : angle 3.20267 / 2.28 ( 1932) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 381 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7819 (mpt-90) REVERT: A 191 PHE cc_start: 0.7583 (OUTLIER) cc_final: 0.7121 (t80) REVERT: A 250 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.6958 (mtpt) REVERT: A 375 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7477 (tm-30) REVERT: A 387 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7273 (mt-10) REVERT: A 407 GLU cc_start: 0.8058 (mp0) cc_final: 0.7163 (pm20) REVERT: B 221 ASP cc_start: 0.8021 (t0) cc_final: 0.7730 (t0) REVERT: B 373 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7008 (mmt) REVERT: B 407 GLU cc_start: 0.8061 (mp0) cc_final: 0.7394 (pm20) REVERT: B 439 GLU cc_start: 0.6230 (OUTLIER) cc_final: 0.5591 (mp0) REVERT: C 193 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.7977 (p) REVERT: C 276 VAL cc_start: 0.8673 (OUTLIER) cc_final: 0.8432 (t) REVERT: C 407 GLU cc_start: 0.8184 (mp0) cc_final: 0.7847 (mp0) REVERT: D 168 GLN cc_start: 0.2154 (OUTLIER) cc_final: 0.1838 (mt0) REVERT: D 250 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.7023 (mtpt) REVERT: D 276 VAL cc_start: 0.8694 (t) cc_final: 0.8445 (t) REVERT: D 373 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.7380 (mtt) REVERT: D 387 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7318 (mt-10) REVERT: D 407 GLU cc_start: 0.8077 (mp0) cc_final: 0.7749 (mp0) outliers start: 52 outliers final: 35 residues processed: 409 average time/residue: 0.7922 time to fit residues: 349.2297 Evaluate side-chains 423 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 378 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ARG Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 287 PHE Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 439 GLU Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 488 ARG Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain D residue 121 HIS Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 168 GLN Chi-restraints excluded: chain D residue 250 LYS Chi-restraints excluded: chain D residue 287 PHE Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain D residue 373 MET Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 501 GLN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 548 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 93 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.0970 chunk 62 optimal weight: 2.9990 chunk 195 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 GLN B 421 GLN C 133 ASN C 412 ASN D 168 GLN D 421 GLN D 436 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.163915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.135572 restraints weight = 19793.539| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.08 r_work: 0.3637 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15600 Z= 0.146 Angle : 0.543 9.691 21148 Z= 0.275 Chirality : 0.046 0.147 2464 Planarity : 0.005 0.053 2776 Dihedral : 3.556 17.310 2220 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.93 % Allowed : 26.54 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.20), residues: 2020 helix: 2.42 (0.18), residues: 812 sheet: 0.66 (0.25), residues: 464 loop : -0.85 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 382 TYR 0.012 0.001 TYR D 126 PHE 0.014 0.001 PHE D 513 TRP 0.009 0.001 TRP D 525 HIS 0.005 0.001 HIS C 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (15600) covalent geometry : angle 0.54343 / 0.28 (21148) hydrogen bonds : bond 0.05348 / 3.69 ( 682) hydrogen bonds : angle 3.35265 / 2.39 ( 1932) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8104.45 seconds wall clock time: 137 minutes 56.69 seconds (8276.69 seconds total)