Starting phenix.real_space_refine on Thu Mar 5 08:29:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jz6_22530/03_2026/7jz6_22530.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jz6_22530/03_2026/7jz6_22530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jz6_22530/03_2026/7jz6_22530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jz6_22530/03_2026/7jz6_22530.map" model { file = "/net/cci-nas-00/data/ceres_data/7jz6_22530/03_2026/7jz6_22530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jz6_22530/03_2026/7jz6_22530.cif" } resolution = 2.53 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.360 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 44 5.16 5 C 13258 2.51 5 N 3589 2.21 5 O 3947 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 238 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20842 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5154 Classifications: {'peptide': 660} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 623} Chain breaks: 1 Chain: "B" Number of atoms: 5166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5166 Classifications: {'peptide': 662} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 625} Chain breaks: 1 Chain: "C" Number of atoms: 5166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5166 Classifications: {'peptide': 662} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 625} Chain breaks: 1 Chain: "D" Number of atoms: 5166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5166 Classifications: {'peptide': 662} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 625} Chain breaks: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 4.85, per 1000 atoms: 0.23 Number of scatterers: 20842 At special positions: 0 Unit cell: (126.36, 98.28, 130.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 44 16.00 O 3947 8.00 N 3589 7.00 C 13258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 834.9 milliseconds 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4830 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 18 sheets defined 57.2% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 61 through 67 Processing helix chain 'A' and resid 70 through 82 Processing helix chain 'A' and resid 91 through 95 Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.637A pdb=" N ARG A 102 " --> pdb=" O GLY A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 Processing helix chain 'A' and resid 129 through 137 Proline residue: A 134 - end of helix removed outlier: 3.993A pdb=" N VAL A 137 " --> pdb=" O PRO A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 145 Processing helix chain 'A' and resid 146 through 154 Processing helix chain 'A' and resid 155 through 157 No H-bonds generated for 'chain 'A' and resid 155 through 157' Processing helix chain 'A' and resid 158 through 173 removed outlier: 4.165A pdb=" N ILE A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 240 through 252 removed outlier: 4.019A pdb=" N ALA A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N MET A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 267 Processing helix chain 'A' and resid 277 through 281 Processing helix chain 'A' and resid 284 through 288 removed outlier: 4.052A pdb=" N ALA A 288 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 293 Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 327 through 335 Processing helix chain 'A' and resid 374 through 383 removed outlier: 4.441A pdb=" N LEU A 380 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 395 removed outlier: 3.931A pdb=" N LYS A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 414 Processing helix chain 'A' and resid 418 through 422 Processing helix chain 'A' and resid 432 through 436 Processing helix chain 'A' and resid 446 through 459 Processing helix chain 'A' and resid 463 through 476 Processing helix chain 'A' and resid 496 through 504 removed outlier: 6.731A pdb=" N ASP A 501 " --> pdb=" O ARG A 498 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL A 502 " --> pdb=" O ASP A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 508 Processing helix chain 'A' and resid 509 through 520 removed outlier: 3.652A pdb=" N LEU A 513 " --> pdb=" O ALA A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 544 removed outlier: 3.663A pdb=" N GLY A 533 " --> pdb=" O ILE A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 564 Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 571 through 573 No H-bonds generated for 'chain 'A' and resid 571 through 573' Processing helix chain 'A' and resid 578 through 581 Processing helix chain 'A' and resid 590 through 602 Processing helix chain 'A' and resid 605 through 619 Processing helix chain 'A' and resid 622 through 626 removed outlier: 3.756A pdb=" N SER A 626 " --> pdb=" O PHE A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 648 Processing helix chain 'A' and resid 678 through 683 Processing helix chain 'A' and resid 684 through 686 No H-bonds generated for 'chain 'A' and resid 684 through 686' Processing helix chain 'A' and resid 687 through 699 removed outlier: 3.662A pdb=" N VAL A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A 696 " --> pdb=" O ALA A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 719 removed outlier: 3.539A pdb=" N PHE A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 61 through 67 Processing helix chain 'B' and resid 70 through 82 Processing helix chain 'B' and resid 91 through 95 Processing helix chain 'B' and resid 96 through 109 removed outlier: 3.523A pdb=" N ARG B 102 " --> pdb=" O GLY B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 127 Processing helix chain 'B' and resid 129 through 137 Proline residue: B 134 - end of helix removed outlier: 3.651A pdb=" N VAL B 137 " --> pdb=" O PRO B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 145 Processing helix chain 'B' and resid 146 through 154 Processing helix chain 'B' and resid 155 through 157 No H-bonds generated for 'chain 'B' and resid 155 through 157' Processing helix chain 'B' and resid 158 through 173 removed outlier: 4.158A pdb=" N ILE B 164 " --> pdb=" O ALA B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 237 through 252 removed outlier: 3.807A pdb=" N ALA B 241 " --> pdb=" O GLU B 237 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B 242 " --> pdb=" O PRO B 238 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ALA B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET B 252 " --> pdb=" O THR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 267 removed outlier: 3.634A pdb=" N HIS B 267 " --> pdb=" O ILE B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 281 Processing helix chain 'B' and resid 284 through 288 removed outlier: 4.095A pdb=" N ALA B 288 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 293 Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 327 through 336 Processing helix chain 'B' and resid 374 through 378 Processing helix chain 'B' and resid 383 through 395 removed outlier: 3.950A pdb=" N LYS B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE B 389 " --> pdb=" O GLU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 414 Processing helix chain 'B' and resid 418 through 422 Processing helix chain 'B' and resid 432 through 436 Processing helix chain 'B' and resid 446 through 459 Processing helix chain 'B' and resid 463 through 476 Processing helix chain 'B' and resid 496 through 504 removed outlier: 6.837A pdb=" N ASP B 501 " --> pdb=" O ARG B 498 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL B 502 " --> pdb=" O ASP B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 508 Processing helix chain 'B' and resid 509 through 520 removed outlier: 3.721A pdb=" N LEU B 513 " --> pdb=" O ALA B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 544 removed outlier: 3.666A pdb=" N GLY B 533 " --> pdb=" O ILE B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 564 Processing helix chain 'B' and resid 565 through 570 Processing helix chain 'B' and resid 571 through 573 No H-bonds generated for 'chain 'B' and resid 571 through 573' Processing helix chain 'B' and resid 578 through 581 Processing helix chain 'B' and resid 590 through 602 Processing helix chain 'B' and resid 605 through 619 Processing helix chain 'B' and resid 622 through 626 removed outlier: 3.798A pdb=" N SER B 626 " --> pdb=" O PHE B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 648 Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 684 through 686 No H-bonds generated for 'chain 'B' and resid 684 through 686' Processing helix chain 'B' and resid 687 through 699 removed outlier: 3.665A pdb=" N VAL B 693 " --> pdb=" O VAL B 689 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL B 696 " --> pdb=" O ALA B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 719 Processing helix chain 'C' and resid 42 through 46 Processing helix chain 'C' and resid 61 through 67 Processing helix chain 'C' and resid 70 through 82 Processing helix chain 'C' and resid 91 through 95 Processing helix chain 'C' and resid 96 through 109 removed outlier: 3.606A pdb=" N ARG C 102 " --> pdb=" O GLY C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 127 Processing helix chain 'C' and resid 129 through 137 Proline residue: C 134 - end of helix Processing helix chain 'C' and resid 138 through 145 removed outlier: 3.669A pdb=" N ALA C 142 " --> pdb=" O SER C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 154 Processing helix chain 'C' and resid 155 through 157 No H-bonds generated for 'chain 'C' and resid 155 through 157' Processing helix chain 'C' and resid 158 through 173 removed outlier: 4.148A pdb=" N ILE C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 Processing helix chain 'C' and resid 240 through 251 removed outlier: 3.941A pdb=" N ALA C 244 " --> pdb=" O SER C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 267 Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 284 through 288 removed outlier: 4.115A pdb=" N ALA C 288 " --> pdb=" O PRO C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 293 Processing helix chain 'C' and resid 305 through 309 Processing helix chain 'C' and resid 327 through 336 Processing helix chain 'C' and resid 374 through 377 Processing helix chain 'C' and resid 378 through 383 removed outlier: 3.902A pdb=" N PHE C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 395 removed outlier: 3.990A pdb=" N LYS C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE C 389 " --> pdb=" O GLU C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 414 Processing helix chain 'C' and resid 418 through 422 Processing helix chain 'C' and resid 432 through 436 Processing helix chain 'C' and resid 446 through 459 Processing helix chain 'C' and resid 463 through 476 Processing helix chain 'C' and resid 496 through 504 removed outlier: 6.947A pdb=" N ASP C 501 " --> pdb=" O ARG C 498 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL C 502 " --> pdb=" O ASP C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 508 Processing helix chain 'C' and resid 509 through 520 removed outlier: 3.631A pdb=" N LEU C 513 " --> pdb=" O ALA C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 544 removed outlier: 3.683A pdb=" N GLY C 533 " --> pdb=" O ILE C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 564 Processing helix chain 'C' and resid 565 through 570 Processing helix chain 'C' and resid 571 through 573 No H-bonds generated for 'chain 'C' and resid 571 through 573' Processing helix chain 'C' and resid 578 through 581 Processing helix chain 'C' and resid 590 through 602 Processing helix chain 'C' and resid 605 through 619 Processing helix chain 'C' and resid 622 through 626 removed outlier: 3.827A pdb=" N SER C 626 " --> pdb=" O PHE C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 648 Processing helix chain 'C' and resid 678 through 683 Processing helix chain 'C' and resid 684 through 686 No H-bonds generated for 'chain 'C' and resid 684 through 686' Processing helix chain 'C' and resid 687 through 699 removed outlier: 3.661A pdb=" N VAL C 693 " --> pdb=" O VAL C 689 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL C 696 " --> pdb=" O ALA C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 719 Processing helix chain 'D' and resid 42 through 46 Processing helix chain 'D' and resid 61 through 67 Processing helix chain 'D' and resid 70 through 82 Processing helix chain 'D' and resid 91 through 95 Processing helix chain 'D' and resid 96 through 109 removed outlier: 3.610A pdb=" N ARG D 102 " --> pdb=" O GLY D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 127 Processing helix chain 'D' and resid 129 through 137 Proline residue: D 134 - end of helix Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'D' and resid 146 through 154 Processing helix chain 'D' and resid 155 through 157 No H-bonds generated for 'chain 'D' and resid 155 through 157' Processing helix chain 'D' and resid 158 through 173 removed outlier: 4.158A pdb=" N ILE D 164 " --> pdb=" O ALA D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 240 through 251 removed outlier: 4.239A pdb=" N ALA D 244 " --> pdb=" O SER D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 267 Processing helix chain 'D' and resid 277 through 281 Processing helix chain 'D' and resid 284 through 288 removed outlier: 4.079A pdb=" N ALA D 288 " --> pdb=" O PRO D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 293 Processing helix chain 'D' and resid 305 through 309 Processing helix chain 'D' and resid 327 through 335 Processing helix chain 'D' and resid 374 through 380 removed outlier: 4.309A pdb=" N LEU D 380 " --> pdb=" O THR D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 395 removed outlier: 3.947A pdb=" N LYS D 388 " --> pdb=" O PRO D 384 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE D 389 " --> pdb=" O GLU D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 414 Processing helix chain 'D' and resid 418 through 422 Processing helix chain 'D' and resid 432 through 436 Processing helix chain 'D' and resid 446 through 459 Processing helix chain 'D' and resid 463 through 476 Processing helix chain 'D' and resid 496 through 504 removed outlier: 6.838A pdb=" N ASP D 501 " --> pdb=" O ARG D 498 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 508 Processing helix chain 'D' and resid 509 through 520 removed outlier: 3.610A pdb=" N LEU D 513 " --> pdb=" O ALA D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 544 removed outlier: 3.696A pdb=" N GLY D 533 " --> pdb=" O ILE D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 565 through 570 Processing helix chain 'D' and resid 571 through 573 No H-bonds generated for 'chain 'D' and resid 571 through 573' Processing helix chain 'D' and resid 578 through 581 Processing helix chain 'D' and resid 590 through 602 Processing helix chain 'D' and resid 605 through 619 Processing helix chain 'D' and resid 622 through 626 removed outlier: 3.813A pdb=" N SER D 626 " --> pdb=" O PHE D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 648 Processing helix chain 'D' and resid 678 through 683 Processing helix chain 'D' and resid 684 through 686 No H-bonds generated for 'chain 'D' and resid 684 through 686' Processing helix chain 'D' and resid 687 through 699 removed outlier: 3.663A pdb=" N VAL D 693 " --> pdb=" O VAL D 689 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL D 696 " --> pdb=" O ALA D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 703 through 719 Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 183 removed outlier: 7.253A pdb=" N PHE A 181 " --> pdb=" O PRO A 425 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 342 Processing sheet with id=AA3, first strand: chain 'A' and resid 359 through 360 removed outlier: 3.535A pdb=" N ILE A 359 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 576 through 577 Processing sheet with id=AA5, first strand: chain 'A' and resid 651 through 655 removed outlier: 3.512A pdb=" N PHE A 675 " --> pdb=" O GLY A 665 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASP A 667 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL A 673 " --> pdb=" O ASP A 667 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 337 through 343 removed outlier: 4.679A pdb=" N GLU B 337 " --> pdb=" O VAL B 353 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA B 347 " --> pdb=" O SER B 343 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 359 through 360 Processing sheet with id=AA8, first strand: chain 'B' and resid 576 through 577 Processing sheet with id=AA9, first strand: chain 'B' and resid 651 through 655 removed outlier: 3.538A pdb=" N PHE B 675 " --> pdb=" O GLY B 665 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASP B 667 " --> pdb=" O VAL B 673 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL B 673 " --> pdb=" O ASP B 667 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 337 through 342 removed outlier: 4.757A pdb=" N GLU C 337 " --> pdb=" O VAL C 353 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C 353 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 359 through 360 Processing sheet with id=AB3, first strand: chain 'C' and resid 576 through 577 Processing sheet with id=AB4, first strand: chain 'C' and resid 651 through 655 removed outlier: 7.132A pdb=" N ASP C 667 " --> pdb=" O VAL C 673 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL C 673 " --> pdb=" O ASP C 667 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 181 through 183 removed outlier: 7.256A pdb=" N PHE D 181 " --> pdb=" O PRO D 425 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 339 through 342 Processing sheet with id=AB7, first strand: chain 'D' and resid 359 through 360 Processing sheet with id=AB8, first strand: chain 'D' and resid 576 through 577 Processing sheet with id=AB9, first strand: chain 'D' and resid 651 through 655 removed outlier: 3.648A pdb=" N PHE D 675 " --> pdb=" O GLY D 665 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ASP D 667 " --> pdb=" O VAL D 673 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL D 673 " --> pdb=" O ASP D 667 " (cutoff:3.500A) 911 hydrogen bonds defined for protein. 2316 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.91 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.33: 4661 1.33 - 1.52: 10007 1.52 - 1.70: 6596 1.70 - 1.89: 88 1.89 - 2.08: 16 Bond restraints: 21368 Sorted by residual: bond pdb=" C VAL C 227 " pdb=" O VAL C 227 " ideal model delta sigma weight residual 1.233 1.138 0.095 1.08e-02 8.57e+03 7.69e+01 bond pdb=" C VAL B 227 " pdb=" O VAL B 227 " ideal model delta sigma weight residual 1.233 1.144 0.089 1.08e-02 8.57e+03 6.78e+01 bond pdb=" C TRP C 89 " pdb=" O TRP C 89 " ideal model delta sigma weight residual 1.238 1.164 0.074 1.28e-02 6.10e+03 3.37e+01 bond pdb=" CA PRO C 90 " pdb=" C PRO C 90 " ideal model delta sigma weight residual 1.521 1.582 -0.061 1.27e-02 6.20e+03 2.32e+01 bond pdb=" C ASN A 280 " pdb=" O ASN A 280 " ideal model delta sigma weight residual 1.236 1.178 0.058 1.29e-02 6.01e+03 2.02e+01 ... (remaining 21363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 28658 3.31 - 6.62: 346 6.62 - 9.94: 49 9.94 - 13.25: 12 13.25 - 16.56: 3 Bond angle restraints: 29068 Sorted by residual: angle pdb=" N VAL B 588 " pdb=" CA VAL B 588 " pdb=" C VAL B 588 " ideal model delta sigma weight residual 110.53 126.23 -15.70 9.40e-01 1.13e+00 2.79e+02 angle pdb=" N ILE D 225 " pdb=" CA ILE D 225 " pdb=" C ILE D 225 " ideal model delta sigma weight residual 110.53 123.63 -13.10 9.40e-01 1.13e+00 1.94e+02 angle pdb=" N GLY C 270 " pdb=" CA GLY C 270 " pdb=" C GLY C 270 " ideal model delta sigma weight residual 111.02 127.58 -16.56 1.86e+00 2.89e-01 7.93e+01 angle pdb=" N GLY B 270 " pdb=" CA GLY B 270 " pdb=" C GLY B 270 " ideal model delta sigma weight residual 111.02 127.14 -16.12 1.86e+00 2.89e-01 7.51e+01 angle pdb=" N VAL D 316 " pdb=" CA VAL D 316 " pdb=" C VAL D 316 " ideal model delta sigma weight residual 108.11 119.44 -11.33 1.40e+00 5.10e-01 6.55e+01 ... (remaining 29063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 10623 17.84 - 35.68: 1297 35.68 - 53.52: 447 53.52 - 71.36: 141 71.36 - 89.21: 42 Dihedral angle restraints: 12550 sinusoidal: 5022 harmonic: 7528 Sorted by residual: dihedral pdb=" C VAL B 588 " pdb=" N VAL B 588 " pdb=" CA VAL B 588 " pdb=" CB VAL B 588 " ideal model delta harmonic sigma weight residual -122.00 -136.41 14.41 0 2.50e+00 1.60e-01 3.32e+01 dihedral pdb=" C GLU D 315 " pdb=" N GLU D 315 " pdb=" CA GLU D 315 " pdb=" CB GLU D 315 " ideal model delta harmonic sigma weight residual -122.60 -134.81 12.21 0 2.50e+00 1.60e-01 2.38e+01 dihedral pdb=" CA ASP D 44 " pdb=" C ASP D 44 " pdb=" N LEU D 45 " pdb=" CA LEU D 45 " ideal model delta harmonic sigma weight residual 180.00 155.81 24.19 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 12547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.360: 3031 0.360 - 0.719: 12 0.719 - 1.079: 0 1.079 - 1.438: 1 1.438 - 1.798: 7 Chirality restraints: 3051 Sorted by residual: chirality pdb=" CG LEU A 662 " pdb=" CB LEU A 662 " pdb=" CD1 LEU A 662 " pdb=" CD2 LEU A 662 " both_signs ideal model delta sigma weight residual False -2.59 -0.79 -1.80 2.00e-01 2.50e+01 8.08e+01 chirality pdb=" CG LEU B 139 " pdb=" CB LEU B 139 " pdb=" CD1 LEU B 139 " pdb=" CD2 LEU B 139 " both_signs ideal model delta sigma weight residual False -2.59 -0.84 -1.75 2.00e-01 2.50e+01 7.68e+01 chirality pdb=" CG LEU A 193 " pdb=" CB LEU A 193 " pdb=" CD1 LEU A 193 " pdb=" CD2 LEU A 193 " both_signs ideal model delta sigma weight residual False -2.59 -0.84 -1.75 2.00e-01 2.50e+01 7.67e+01 ... (remaining 3048 not shown) Planarity restraints: 3825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP C 89 " 0.064 5.00e-02 4.00e+02 9.70e-02 1.51e+01 pdb=" N PRO C 90 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO C 90 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 90 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 89 " -0.054 5.00e-02 4.00e+02 8.20e-02 1.08e+01 pdb=" N PRO B 90 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO B 90 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 90 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP D 89 " 0.052 5.00e-02 4.00e+02 7.86e-02 9.87e+00 pdb=" N PRO D 90 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO D 90 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 90 " 0.044 5.00e-02 4.00e+02 ... (remaining 3822 not shown) Histogram of nonbonded interaction distances: 1.22 - 1.96: 8 1.96 - 2.69: 766 2.69 - 3.43: 29844 3.43 - 4.16: 52071 4.16 - 4.90: 91585 Nonbonded interactions: 174274 Sorted by model distance: nonbonded pdb=" CH2 TRP D 105 " pdb=" CE2 TYR D 226 " model vdw 1.219 3.640 nonbonded pdb=" CH2 TRP B 105 " pdb=" CE2 TYR B 226 " model vdw 1.296 3.640 nonbonded pdb=" CH2 TRP C 105 " pdb=" CE2 TYR C 226 " model vdw 1.310 3.640 nonbonded pdb=" CH2 TRP A 105 " pdb=" CE2 TYR A 226 " model vdw 1.357 3.640 nonbonded pdb=" OG1 THR A 323 " pdb=" OE1 GLN A 324 " model vdw 1.865 3.040 ... (remaining 174269 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 38 through 195 or resid 224 through 1001)) selection = (chain 'C' and (resid 38 through 195 or resid 224 through 1001)) selection = (chain 'D' and (resid 38 through 195 or resid 224 through 1001)) } 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: 0.010 Normalize map: mean=0, sd=1: 0.040 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.630 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6315 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 : 0.010 0.338 21372 Z= 0.436 Angle : 1.038 16.560 29068 Z= 0.598 Chirality : 0.106 1.798 3051 Planarity : 0.007 0.097 3825 Dihedral : 19.126 89.205 7720 Min Nonbonded Distance : 1.219 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 11.17 % Allowed : 17.34 % Favored : 71.48 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 5.56 % 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: -3.03 (0.14), residues: 2630 helix: -1.92 (0.12), residues: 1108 sheet: -0.37 (0.56), residues: 78 loop : -2.21 (0.14), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 634 TYR 0.037 0.004 TYR C 226 PHE 0.029 0.004 PHE B 675 TRP 0.024 0.004 TRP C 88 HIS 0.013 0.004 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00867 (21368) covalent geometry : angle 1.03776 (29068) hydrogen bonds : bond 0.18197 ( 911) hydrogen bonds : angle 6.37580 ( 2316) Misc. bond : bond 0.33222 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 239 poor density : 387 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.5049 (OUTLIER) cc_final: 0.4656 (pm20) REVERT: A 141 LYS cc_start: 0.7726 (mttp) cc_final: 0.7518 (mttp) REVERT: A 144 ARG cc_start: 0.7223 (OUTLIER) cc_final: 0.6905 (tpp-160) REVERT: A 358 ILE cc_start: 0.5856 (OUTLIER) cc_final: 0.5559 (pt) REVERT: A 396 ASP cc_start: 0.5786 (OUTLIER) cc_final: 0.5480 (t0) REVERT: A 414 ARG cc_start: 0.7162 (ptt180) cc_final: 0.6684 (ptt180) REVERT: A 421 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7319 (mtp-110) REVERT: A 454 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7417 (mtpm) REVERT: A 522 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.6661 (mptp) REVERT: A 581 ASN cc_start: 0.7343 (OUTLIER) cc_final: 0.7088 (t0) REVERT: A 623 PHE cc_start: 0.6929 (OUTLIER) cc_final: 0.6484 (p90) REVERT: A 708 LYS cc_start: 0.7376 (mtmt) cc_final: 0.7097 (mptt) REVERT: B 68 LYS cc_start: 0.7525 (mttt) cc_final: 0.7290 (mttm) REVERT: B 144 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.6893 (tpp-160) REVERT: B 156 LYS cc_start: 0.7276 (OUTLIER) cc_final: 0.6930 (ttmt) REVERT: B 286 GLU cc_start: 0.6008 (OUTLIER) cc_final: 0.5517 (mm-30) REVERT: B 381 ARG cc_start: 0.5654 (OUTLIER) cc_final: 0.5420 (tpt-90) REVERT: B 414 ARG cc_start: 0.7174 (ptt180) cc_final: 0.6754 (ptt180) REVERT: B 452 ASP cc_start: 0.6558 (m-30) cc_final: 0.5870 (t0) REVERT: B 454 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7338 (mtpm) REVERT: B 522 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.6537 (mptp) REVERT: B 623 PHE cc_start: 0.6695 (OUTLIER) cc_final: 0.6210 (p90) REVERT: C 42 ARG cc_start: 0.6025 (mmm-85) cc_final: 0.5782 (mmt90) REVERT: C 144 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.6821 (tpp-160) REVERT: C 156 LYS cc_start: 0.7270 (mtmm) cc_final: 0.6783 (mtmt) REVERT: C 414 ARG cc_start: 0.7020 (ptt180) cc_final: 0.6614 (ptt180) REVERT: C 571 LEU cc_start: 0.6996 (mt) cc_final: 0.6753 (mt) REVERT: C 575 ILE cc_start: 0.6743 (OUTLIER) cc_final: 0.6432 (mm) REVERT: C 623 PHE cc_start: 0.6613 (OUTLIER) cc_final: 0.6125 (p90) REVERT: C 648 ASP cc_start: 0.6738 (OUTLIER) cc_final: 0.6383 (t0) REVERT: C 667 ASP cc_start: 0.5439 (OUTLIER) cc_final: 0.5062 (t0) REVERT: C 705 LYS cc_start: 0.6860 (OUTLIER) cc_final: 0.6536 (tttm) REVERT: C 708 LYS cc_start: 0.7327 (mtmt) cc_final: 0.7051 (tptp) REVERT: D 42 ARG cc_start: 0.6065 (mmm-85) cc_final: 0.5852 (mmt90) REVERT: D 58 GLU cc_start: 0.5375 (OUTLIER) cc_final: 0.4524 (pm20) REVERT: D 64 LYS cc_start: 0.6128 (ttmm) cc_final: 0.5836 (ttmm) REVERT: D 68 LYS cc_start: 0.7370 (mttt) cc_final: 0.7128 (mttm) REVERT: D 103 MET cc_start: 0.7448 (ttp) cc_final: 0.7208 (ttm) REVERT: D 133 TRP cc_start: 0.5721 (m-10) cc_final: 0.5462 (m-10) REVERT: D 144 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6930 (tpp-160) REVERT: D 299 SER cc_start: 0.5310 (OUTLIER) cc_final: 0.5002 (t) REVERT: D 414 ARG cc_start: 0.7232 (ptt180) cc_final: 0.6877 (ptt180) REVERT: D 539 LYS cc_start: 0.6850 (tttp) cc_final: 0.6517 (mtpp) REVERT: D 565 ASP cc_start: 0.6421 (t70) cc_final: 0.6055 (t0) REVERT: D 623 PHE cc_start: 0.6701 (OUTLIER) cc_final: 0.5937 (p90) REVERT: D 666 ARG cc_start: 0.5233 (OUTLIER) cc_final: 0.4813 (ptp-170) REVERT: D 674 LYS cc_start: 0.7039 (tttp) cc_final: 0.6706 (tttm) REVERT: D 705 LYS cc_start: 0.6860 (OUTLIER) cc_final: 0.6248 (tttt) REVERT: D 708 LYS cc_start: 0.7275 (mtmt) cc_final: 0.7060 (mptt) outliers start: 239 outliers final: 156 residues processed: 585 average time/residue: 0.6847 time to fit residues: 445.1715 Evaluate side-chains 550 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 366 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 126 ARG Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 421 ARG Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 522 LYS Chi-restraints excluded: chain A residue 581 ASN Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 654 LYS Chi-restraints excluded: chain A residue 668 ARG Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 156 LYS Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 454 LYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 598 LYS Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 342 ARG Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 419 LYS Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 580 ARG Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 598 LYS Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 667 ASP Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 700 SER Chi-restraints excluded: chain C residue 705 LYS Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 320 GLN Chi-restraints excluded: chain D residue 342 ARG Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 419 LYS Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 589 SER Chi-restraints excluded: chain D residue 592 GLU Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain D residue 634 ARG Chi-restraints excluded: chain D residue 637 VAL Chi-restraints excluded: chain D residue 648 ASP Chi-restraints excluded: chain D residue 656 THR Chi-restraints excluded: chain D residue 659 SER Chi-restraints excluded: chain D residue 666 ARG Chi-restraints excluded: chain D residue 668 ARG Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 686 SER Chi-restraints excluded: chain D residue 700 SER Chi-restraints excluded: chain D residue 705 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN A 332 ASN B 125 GLN B 645 ASN C 628 ASN C 645 ASN D 280 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.188362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.169806 restraints weight = 181223.863| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 5.48 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 21372 Z= 0.209 Angle : 0.738 14.661 29068 Z= 0.383 Chirality : 0.046 0.184 3051 Planarity : 0.006 0.063 3825 Dihedral : 13.496 90.905 3289 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 7.53 % Allowed : 20.15 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.30 (0.15), residues: 2630 helix: -0.34 (0.14), residues: 1094 sheet: -0.19 (0.53), residues: 78 loop : -1.30 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 580 TYR 0.013 0.003 TYR A 226 PHE 0.020 0.003 PHE A 675 TRP 0.020 0.002 TRP C 338 HIS 0.013 0.002 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00468 (21368) covalent geometry : angle 0.73835 (29068) hydrogen bonds : bond 0.06602 ( 911) hydrogen bonds : angle 4.89667 ( 2316) Misc. bond : bond 0.05685 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 383 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.4886 (OUTLIER) cc_final: 0.4647 (pm20) REVERT: A 64 LYS cc_start: 0.6223 (mtpm) cc_final: 0.5978 (ttmm) REVERT: A 68 LYS cc_start: 0.7427 (mttt) cc_final: 0.7139 (mttp) REVERT: A 144 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.6897 (tpp-160) REVERT: A 381 ARG cc_start: 0.5671 (OUTLIER) cc_final: 0.5407 (tpt-90) REVERT: A 396 ASP cc_start: 0.5580 (OUTLIER) cc_final: 0.5332 (t0) REVERT: A 421 ARG cc_start: 0.7585 (mtm110) cc_final: 0.7299 (mtp-110) REVERT: A 454 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7225 (mtpm) REVERT: A 479 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6585 (mtp180) REVERT: A 567 GLU cc_start: 0.5374 (tp30) cc_final: 0.4749 (mp0) REVERT: A 575 ILE cc_start: 0.6363 (pp) cc_final: 0.6103 (mm) REVERT: A 580 ARG cc_start: 0.7582 (ptt180) cc_final: 0.7150 (ptm160) REVERT: A 623 PHE cc_start: 0.6518 (OUTLIER) cc_final: 0.5818 (p90) REVERT: A 708 LYS cc_start: 0.7402 (mtmt) cc_final: 0.6881 (mmtt) REVERT: B 75 LYS cc_start: 0.6934 (OUTLIER) cc_final: 0.6348 (mttp) REVERT: B 144 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6869 (tpp-160) REVERT: B 156 LYS cc_start: 0.7303 (mtmm) cc_final: 0.6837 (mtmt) REVERT: B 299 SER cc_start: 0.6065 (OUTLIER) cc_final: 0.5722 (t) REVERT: B 452 ASP cc_start: 0.6640 (m-30) cc_final: 0.5921 (t0) REVERT: B 454 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7360 (mtmm) REVERT: B 522 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.6567 (mptp) REVERT: B 581 ASN cc_start: 0.7269 (t0) cc_final: 0.6866 (t0) REVERT: B 623 PHE cc_start: 0.6264 (OUTLIER) cc_final: 0.5689 (p90) REVERT: B 674 LYS cc_start: 0.7096 (tttm) cc_final: 0.6885 (tttm) REVERT: C 42 ARG cc_start: 0.5924 (mmm-85) cc_final: 0.5638 (mmt90) REVERT: C 64 LYS cc_start: 0.6045 (ttmm) cc_final: 0.5713 (ttmm) REVERT: C 144 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.7023 (tpp-160) REVERT: C 156 LYS cc_start: 0.7360 (mtmm) cc_final: 0.6805 (mtmt) REVERT: C 299 SER cc_start: 0.5890 (OUTLIER) cc_final: 0.5659 (t) REVERT: C 342 ARG cc_start: 0.5723 (OUTLIER) cc_final: 0.4879 (mmm160) REVERT: C 519 GLU cc_start: 0.6444 (mm-30) cc_final: 0.6086 (mm-30) REVERT: C 571 LEU cc_start: 0.7068 (mt) cc_final: 0.6775 (mt) REVERT: C 575 ILE cc_start: 0.6768 (OUTLIER) cc_final: 0.6253 (mm) REVERT: C 581 ASN cc_start: 0.7066 (t0) cc_final: 0.6755 (t0) REVERT: C 623 PHE cc_start: 0.6133 (OUTLIER) cc_final: 0.5562 (p90) REVERT: C 708 LYS cc_start: 0.7284 (mtmt) cc_final: 0.6874 (mmtt) REVERT: D 64 LYS cc_start: 0.5831 (ttmm) cc_final: 0.5559 (ttmm) REVERT: D 68 LYS cc_start: 0.7221 (mttt) cc_final: 0.6925 (mttm) REVERT: D 79 LYS cc_start: 0.7011 (OUTLIER) cc_final: 0.6699 (ttpt) REVERT: D 144 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.6960 (tpp-160) REVERT: D 479 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.6674 (mtp180) REVERT: D 539 LYS cc_start: 0.6868 (tttp) cc_final: 0.6491 (mtpp) REVERT: D 565 ASP cc_start: 0.6233 (t70) cc_final: 0.5813 (t0) REVERT: D 623 PHE cc_start: 0.6762 (OUTLIER) cc_final: 0.6364 (p90) REVERT: D 674 LYS cc_start: 0.7385 (tttp) cc_final: 0.6867 (tttm) REVERT: D 708 LYS cc_start: 0.7154 (mtmt) cc_final: 0.6750 (mmtt) outliers start: 161 outliers final: 94 residues processed: 512 average time/residue: 0.6501 time to fit residues: 372.4840 Evaluate side-chains 482 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 366 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 454 LYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 522 LYS Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 598 LYS Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 342 ARG Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 419 LYS Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 474 SER Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 598 LYS Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 419 LYS Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 589 SER Chi-restraints excluded: chain D residue 592 GLU Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 634 ARG Chi-restraints excluded: chain D residue 637 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 258 optimal weight: 7.9990 chunk 71 optimal weight: 0.0870 chunk 144 optimal weight: 7.9990 chunk 48 optimal weight: 20.0000 chunk 128 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 158 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 37 optimal weight: 0.3980 chunk 169 optimal weight: 5.9990 chunk 241 optimal weight: 8.9990 overall best weight: 4.4964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 398 GLN D 251 ASN D 280 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.188541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.170206 restraints weight = 180218.905| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 5.44 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 21372 Z= 0.183 Angle : 0.678 13.685 29068 Z= 0.350 Chirality : 0.045 0.172 3051 Planarity : 0.006 0.054 3825 Dihedral : 11.640 87.470 3120 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 6.40 % Allowed : 22.02 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.67 (0.15), residues: 2630 helix: 0.24 (0.15), residues: 1093 sheet: -0.11 (0.53), residues: 78 loop : -0.98 (0.16), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 583 TYR 0.022 0.002 TYR A 226 PHE 0.016 0.002 PHE C 675 TRP 0.019 0.002 TRP B 338 HIS 0.010 0.002 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00407 (21368) covalent geometry : angle 0.67770 (29068) hydrogen bonds : bond 0.06035 ( 911) hydrogen bonds : angle 4.64995 ( 2316) Misc. bond : bond 0.03591 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 372 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 58 GLU cc_start: 0.5003 (OUTLIER) cc_final: 0.4776 (pm20) REVERT: A 64 LYS cc_start: 0.6115 (mtpm) cc_final: 0.5637 (ttpp) REVERT: A 75 LYS cc_start: 0.7094 (OUTLIER) cc_final: 0.6740 (mttp) REVERT: A 144 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6935 (tpp-160) REVERT: A 156 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.6833 (mtmt) REVERT: A 396 ASP cc_start: 0.5484 (OUTLIER) cc_final: 0.5232 (t0) REVERT: A 414 ARG cc_start: 0.7004 (ptt180) cc_final: 0.6660 (ptt180) REVERT: A 454 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.7294 (mtmm) REVERT: A 567 GLU cc_start: 0.5630 (tp30) cc_final: 0.4953 (mp0) REVERT: A 623 PHE cc_start: 0.6567 (OUTLIER) cc_final: 0.6127 (p90) REVERT: A 708 LYS cc_start: 0.7224 (mtmt) cc_final: 0.6838 (tptp) REVERT: B 144 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.6936 (tpp-160) REVERT: B 156 LYS cc_start: 0.7242 (mtmm) cc_final: 0.6715 (mtmt) REVERT: B 299 SER cc_start: 0.5748 (OUTLIER) cc_final: 0.5400 (t) REVERT: B 452 ASP cc_start: 0.6636 (m-30) cc_final: 0.5977 (t0) REVERT: B 581 ASN cc_start: 0.7094 (t0) cc_final: 0.6841 (t0) REVERT: C 42 ARG cc_start: 0.5926 (mmm-85) cc_final: 0.5608 (mmt90) REVERT: C 75 LYS cc_start: 0.7164 (OUTLIER) cc_final: 0.6654 (mttp) REVERT: C 144 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6850 (tpp-160) REVERT: C 156 LYS cc_start: 0.7376 (mtmm) cc_final: 0.6848 (mtmt) REVERT: C 299 SER cc_start: 0.5884 (OUTLIER) cc_final: 0.5585 (t) REVERT: C 342 ARG cc_start: 0.5748 (OUTLIER) cc_final: 0.5268 (mmm160) REVERT: C 359 ILE cc_start: 0.5917 (OUTLIER) cc_final: 0.5577 (mp) REVERT: C 519 GLU cc_start: 0.6463 (mm-30) cc_final: 0.6120 (mm-30) REVERT: C 571 LEU cc_start: 0.7147 (mt) cc_final: 0.6917 (mt) REVERT: C 575 ILE cc_start: 0.6664 (OUTLIER) cc_final: 0.6172 (mm) REVERT: C 581 ASN cc_start: 0.7093 (t0) cc_final: 0.6884 (t0) REVERT: C 708 LYS cc_start: 0.7187 (mtmt) cc_final: 0.6834 (mmtt) REVERT: D 64 LYS cc_start: 0.5938 (ttmm) cc_final: 0.5637 (ttmm) REVERT: D 68 LYS cc_start: 0.7555 (mttt) cc_final: 0.7240 (mttm) REVERT: D 163 PHE cc_start: 0.7592 (m-80) cc_final: 0.7350 (m-80) REVERT: D 447 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6587 (tt0) REVERT: D 479 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.6537 (mtp180) REVERT: D 539 LYS cc_start: 0.6736 (tttp) cc_final: 0.6324 (mtpp) REVERT: D 623 PHE cc_start: 0.6814 (OUTLIER) cc_final: 0.6259 (p90) REVERT: D 634 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.7022 (ptt180) REVERT: D 674 LYS cc_start: 0.7430 (tttp) cc_final: 0.6837 (tttm) REVERT: D 708 LYS cc_start: 0.7234 (mtmt) cc_final: 0.6787 (mmtt) REVERT: D 721 ASP cc_start: 0.7386 (p0) cc_final: 0.7161 (p0) outliers start: 137 outliers final: 79 residues processed: 483 average time/residue: 0.6412 time to fit residues: 346.2541 Evaluate side-chains 463 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 365 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 598 LYS Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 342 ARG Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 598 LYS Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 320 GLN Chi-restraints excluded: chain D residue 342 ARG Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 592 GLU Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 634 ARG Chi-restraints excluded: chain D residue 637 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 51 optimal weight: 9.9990 chunk 181 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 244 optimal weight: 5.9990 chunk 226 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN D 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.188845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.170335 restraints weight = 179901.625| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 5.45 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 21372 Z= 0.167 Angle : 0.646 13.288 29068 Z= 0.333 Chirality : 0.044 0.153 3051 Planarity : 0.006 0.054 3825 Dihedral : 10.739 88.135 3049 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 6.31 % Allowed : 22.30 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.45 (0.15), residues: 2630 helix: 0.44 (0.14), residues: 1129 sheet: -0.02 (0.53), residues: 78 loop : -0.90 (0.16), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 560 TYR 0.021 0.002 TYR A 226 PHE 0.016 0.002 PHE A 675 TRP 0.018 0.002 TRP B 338 HIS 0.009 0.002 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00371 (21368) covalent geometry : angle 0.64558 (29068) hydrogen bonds : bond 0.05691 ( 911) hydrogen bonds : angle 4.50951 ( 2316) Misc. bond : bond 0.03754 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 368 time to evaluate : 0.695 Fit side-chains REVERT: A 64 LYS cc_start: 0.6337 (mtpm) cc_final: 0.6129 (ttmm) REVERT: A 75 LYS cc_start: 0.7129 (OUTLIER) cc_final: 0.6744 (mttp) REVERT: A 144 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.6983 (tpp-160) REVERT: A 292 GLU cc_start: 0.5700 (mm-30) cc_final: 0.5453 (mp0) REVERT: A 396 ASP cc_start: 0.5317 (OUTLIER) cc_final: 0.5097 (t0) REVERT: A 454 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7375 (mtmm) REVERT: A 623 PHE cc_start: 0.6636 (OUTLIER) cc_final: 0.6109 (p90) REVERT: A 708 LYS cc_start: 0.7116 (mtmt) cc_final: 0.6687 (mmtt) REVERT: B 144 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6950 (tpp-160) REVERT: B 156 LYS cc_start: 0.7071 (mtmm) cc_final: 0.6614 (mtmt) REVERT: B 299 SER cc_start: 0.5626 (OUTLIER) cc_final: 0.5342 (t) REVERT: B 452 ASP cc_start: 0.6515 (m-30) cc_final: 0.5909 (t0) REVERT: B 454 LYS cc_start: 0.7507 (OUTLIER) cc_final: 0.7063 (mttt) REVERT: B 575 ILE cc_start: 0.6749 (OUTLIER) cc_final: 0.6267 (mm) REVERT: B 581 ASN cc_start: 0.6947 (t0) cc_final: 0.6662 (t0) REVERT: B 623 PHE cc_start: 0.6491 (OUTLIER) cc_final: 0.6189 (p90) REVERT: B 674 LYS cc_start: 0.7370 (tttp) cc_final: 0.7012 (tttm) REVERT: B 721 ASP cc_start: 0.7378 (p0) cc_final: 0.7166 (p0) REVERT: C 42 ARG cc_start: 0.6019 (mmm-85) cc_final: 0.5710 (mmt90) REVERT: C 75 LYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6628 (mttp) REVERT: C 144 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.6856 (tpp-160) REVERT: C 156 LYS cc_start: 0.7257 (mtmm) cc_final: 0.6712 (mtmt) REVERT: C 163 PHE cc_start: 0.7570 (m-80) cc_final: 0.7366 (m-80) REVERT: C 227 VAL cc_start: 0.5584 (m) cc_final: 0.5045 (t) REVERT: C 299 SER cc_start: 0.6011 (OUTLIER) cc_final: 0.5773 (t) REVERT: C 359 ILE cc_start: 0.5851 (OUTLIER) cc_final: 0.5522 (mp) REVERT: C 562 ASP cc_start: 0.5339 (p0) cc_final: 0.5076 (p0) REVERT: C 575 ILE cc_start: 0.6427 (OUTLIER) cc_final: 0.5941 (mm) REVERT: C 581 ASN cc_start: 0.6969 (t0) cc_final: 0.6730 (t0) REVERT: C 708 LYS cc_start: 0.7132 (mtmt) cc_final: 0.6672 (mmtt) REVERT: D 64 LYS cc_start: 0.6163 (ttmm) cc_final: 0.5819 (ttmm) REVERT: D 68 LYS cc_start: 0.7459 (mttt) cc_final: 0.7137 (mttm) REVERT: D 163 PHE cc_start: 0.7611 (m-80) cc_final: 0.7352 (m-80) REVERT: D 252 MET cc_start: 0.5108 (mtt) cc_final: 0.4851 (mtt) REVERT: D 335 LYS cc_start: 0.5406 (OUTLIER) cc_final: 0.5104 (tmtt) REVERT: D 447 GLU cc_start: 0.6687 (OUTLIER) cc_final: 0.6394 (tt0) REVERT: D 479 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.6674 (mtp180) REVERT: D 539 LYS cc_start: 0.6770 (tttp) cc_final: 0.6376 (mtpp) REVERT: D 565 ASP cc_start: 0.6090 (t70) cc_final: 0.5674 (t0) REVERT: D 623 PHE cc_start: 0.6607 (OUTLIER) cc_final: 0.6247 (p90) REVERT: D 634 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.7097 (ptt180) REVERT: D 674 LYS cc_start: 0.7325 (tttp) cc_final: 0.6802 (tttm) REVERT: D 708 LYS cc_start: 0.7147 (mtmt) cc_final: 0.6708 (mmtt) outliers start: 135 outliers final: 79 residues processed: 475 average time/residue: 0.6451 time to fit residues: 342.5010 Evaluate side-chains 455 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 356 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 454 LYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 598 LYS Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 144 ARG Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 598 LYS Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 320 GLN Chi-restraints excluded: chain D residue 335 LYS Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 592 GLU Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 634 ARG Chi-restraints excluded: chain D residue 637 VAL Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 700 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 204 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 252 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 122 optimal weight: 20.0000 chunk 72 optimal weight: 8.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 324 GLN D 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.190711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.172136 restraints weight = 180370.521| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 5.47 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 21372 Z= 0.132 Angle : 0.589 12.129 29068 Z= 0.302 Chirality : 0.042 0.154 3051 Planarity : 0.005 0.054 3825 Dihedral : 10.069 79.979 3033 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 5.80 % Allowed : 22.67 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.09 (0.16), residues: 2630 helix: 0.80 (0.15), residues: 1129 sheet: 1.13 (0.58), residues: 48 loop : -0.78 (0.16), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 185 TYR 0.026 0.002 TYR D 226 PHE 0.015 0.002 PHE B 163 TRP 0.015 0.002 TRP A 189 HIS 0.007 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00289 (21368) covalent geometry : angle 0.58935 (29068) hydrogen bonds : bond 0.04876 ( 911) hydrogen bonds : angle 4.33452 ( 2316) Misc. bond : bond 0.05568 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 373 time to evaluate : 0.818 Fit side-chains REVERT: A 75 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6872 (mttp) REVERT: A 144 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.6786 (tpp-160) REVERT: A 292 GLU cc_start: 0.5903 (mm-30) cc_final: 0.5679 (mp0) REVERT: A 317 VAL cc_start: 0.6829 (t) cc_final: 0.6457 (p) REVERT: A 342 ARG cc_start: 0.5461 (OUTLIER) cc_final: 0.5209 (ptp-110) REVERT: A 396 ASP cc_start: 0.5486 (OUTLIER) cc_final: 0.5271 (t0) REVERT: A 479 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.6813 (mtp180) REVERT: A 580 ARG cc_start: 0.7620 (ptt180) cc_final: 0.7233 (ptm160) REVERT: A 598 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.6722 (tmtp) REVERT: A 622 ASN cc_start: 0.7348 (m-40) cc_final: 0.7142 (m-40) REVERT: A 627 LYS cc_start: 0.7532 (mtpt) cc_final: 0.7153 (mtpp) REVERT: A 708 LYS cc_start: 0.7193 (mtmt) cc_final: 0.6736 (mmtt) REVERT: B 41 LEU cc_start: 0.5888 (OUTLIER) cc_final: 0.5623 (tp) REVERT: B 93 TRP cc_start: 0.6360 (m-90) cc_final: 0.6020 (m-90) REVERT: B 141 LYS cc_start: 0.7409 (OUTLIER) cc_final: 0.6795 (mptm) REVERT: B 144 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6895 (tpp-160) REVERT: B 156 LYS cc_start: 0.7233 (mtmm) cc_final: 0.6791 (mtmt) REVERT: B 163 PHE cc_start: 0.7760 (m-80) cc_final: 0.7559 (m-80) REVERT: B 299 SER cc_start: 0.5496 (OUTLIER) cc_final: 0.5204 (t) REVERT: B 448 GLN cc_start: 0.7209 (OUTLIER) cc_final: 0.6993 (tp40) REVERT: B 452 ASP cc_start: 0.6389 (m-30) cc_final: 0.5682 (t70) REVERT: B 479 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.6694 (mtp180) REVERT: B 575 ILE cc_start: 0.6775 (OUTLIER) cc_final: 0.6230 (mm) REVERT: B 581 ASN cc_start: 0.7111 (t0) cc_final: 0.6780 (t0) REVERT: B 598 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.6568 (tmtp) REVERT: B 622 ASN cc_start: 0.7266 (m-40) cc_final: 0.6991 (m-40) REVERT: B 667 ASP cc_start: 0.4941 (OUTLIER) cc_final: 0.4681 (t70) REVERT: B 674 LYS cc_start: 0.7313 (tttp) cc_final: 0.7007 (tttm) REVERT: C 75 LYS cc_start: 0.7151 (OUTLIER) cc_final: 0.6697 (mttp) REVERT: C 156 LYS cc_start: 0.7232 (mtmm) cc_final: 0.6730 (mtmt) REVERT: C 163 PHE cc_start: 0.7646 (m-80) cc_final: 0.7425 (m-80) REVERT: C 227 VAL cc_start: 0.5426 (m) cc_final: 0.4887 (t) REVERT: C 299 SER cc_start: 0.5932 (OUTLIER) cc_final: 0.5677 (t) REVERT: C 317 VAL cc_start: 0.6982 (t) cc_final: 0.6538 (p) REVERT: C 479 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.6771 (mtp180) REVERT: C 562 ASP cc_start: 0.5399 (p0) cc_final: 0.5183 (p0) REVERT: C 575 ILE cc_start: 0.6525 (OUTLIER) cc_final: 0.5931 (mm) REVERT: C 581 ASN cc_start: 0.7011 (t0) cc_final: 0.6763 (t0) REVERT: C 598 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.6584 (tmtp) REVERT: C 708 LYS cc_start: 0.7200 (mtmt) cc_final: 0.6723 (mmtt) REVERT: D 335 LYS cc_start: 0.5382 (OUTLIER) cc_final: 0.5081 (tmtt) REVERT: D 447 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6549 (tt0) REVERT: D 448 GLN cc_start: 0.6924 (OUTLIER) cc_final: 0.6710 (tp40) REVERT: D 452 ASP cc_start: 0.6457 (m-30) cc_final: 0.5886 (t70) REVERT: D 479 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6884 (mtp180) REVERT: D 539 LYS cc_start: 0.6617 (tttp) cc_final: 0.6179 (mtpp) REVERT: D 562 ASP cc_start: 0.5497 (p0) cc_final: 0.5207 (p0) REVERT: D 565 ASP cc_start: 0.6135 (t70) cc_final: 0.5759 (t0) REVERT: D 598 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.6517 (tmtp) REVERT: D 623 PHE cc_start: 0.6577 (OUTLIER) cc_final: 0.6018 (p90) REVERT: D 634 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.7289 (ptt180) REVERT: D 673 VAL cc_start: 0.6698 (OUTLIER) cc_final: 0.6460 (t) REVERT: D 674 LYS cc_start: 0.7196 (tttp) cc_final: 0.6652 (tttm) REVERT: D 708 LYS cc_start: 0.7066 (mtmt) cc_final: 0.6705 (mmtt) outliers start: 124 outliers final: 62 residues processed: 474 average time/residue: 0.6349 time to fit residues: 336.9423 Evaluate side-chains 453 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 363 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 598 LYS Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 598 LYS Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 681 ASP Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 320 GLN Chi-restraints excluded: chain D residue 335 LYS Chi-restraints excluded: chain D residue 342 ARG Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 592 GLU Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 634 ARG Chi-restraints excluded: chain D residue 637 VAL Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 700 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 229 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 260 optimal weight: 9.9990 chunk 250 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 154 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 170 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN D 280 ASN D 324 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.187863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.169038 restraints weight = 178037.089| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 5.43 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 21372 Z= 0.209 Angle : 0.705 13.228 29068 Z= 0.366 Chirality : 0.046 0.162 3051 Planarity : 0.006 0.055 3825 Dihedral : 9.959 86.594 3006 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 6.12 % Allowed : 22.81 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.39 (0.15), residues: 2630 helix: 0.48 (0.14), residues: 1129 sheet: 1.30 (0.57), residues: 48 loop : -0.89 (0.16), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 560 TYR 0.018 0.003 TYR D 226 PHE 0.014 0.002 PHE B 675 TRP 0.018 0.003 TRP A 189 HIS 0.008 0.002 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00470 (21368) covalent geometry : angle 0.70546 (29068) hydrogen bonds : bond 0.06469 ( 911) hydrogen bonds : angle 4.54984 ( 2316) Misc. bond : bond 0.01657 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 363 time to evaluate : 0.724 Fit side-chains REVERT: A 64 LYS cc_start: 0.5907 (ttmm) cc_final: 0.5703 (ttpp) REVERT: A 75 LYS cc_start: 0.7062 (OUTLIER) cc_final: 0.6584 (mttp) REVERT: A 144 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6891 (tpp-160) REVERT: A 292 GLU cc_start: 0.6022 (mm-30) cc_final: 0.5789 (mp0) REVERT: A 317 VAL cc_start: 0.6811 (t) cc_final: 0.6400 (p) REVERT: A 335 LYS cc_start: 0.5517 (OUTLIER) cc_final: 0.5175 (tmtt) REVERT: A 342 ARG cc_start: 0.5412 (OUTLIER) cc_final: 0.5150 (ptp-110) REVERT: A 414 ARG cc_start: 0.6941 (ptt180) cc_final: 0.6559 (ptt180) REVERT: A 454 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.7078 (mttt) REVERT: A 623 PHE cc_start: 0.6565 (OUTLIER) cc_final: 0.6197 (p90) REVERT: A 708 LYS cc_start: 0.7261 (mtmt) cc_final: 0.6842 (tptp) REVERT: B 144 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.7025 (tpp-160) REVERT: B 156 LYS cc_start: 0.7320 (mtmm) cc_final: 0.6824 (mtmt) REVERT: B 299 SER cc_start: 0.5463 (OUTLIER) cc_final: 0.5219 (t) REVERT: B 452 ASP cc_start: 0.6703 (m-30) cc_final: 0.6026 (t0) REVERT: B 575 ILE cc_start: 0.6812 (OUTLIER) cc_final: 0.6283 (mm) REVERT: B 581 ASN cc_start: 0.7175 (t0) cc_final: 0.6853 (t0) REVERT: B 623 PHE cc_start: 0.6718 (OUTLIER) cc_final: 0.6409 (p90) REVERT: B 667 ASP cc_start: 0.4977 (OUTLIER) cc_final: 0.4687 (t70) REVERT: C 75 LYS cc_start: 0.7127 (OUTLIER) cc_final: 0.6590 (mttp) REVERT: C 156 LYS cc_start: 0.7380 (mtmm) cc_final: 0.6850 (mtmt) REVERT: C 299 SER cc_start: 0.5972 (OUTLIER) cc_final: 0.5745 (t) REVERT: C 562 ASP cc_start: 0.5351 (p0) cc_final: 0.5137 (p0) REVERT: C 575 ILE cc_start: 0.6638 (OUTLIER) cc_final: 0.6200 (mm) REVERT: C 581 ASN cc_start: 0.6985 (t0) cc_final: 0.6724 (t0) REVERT: C 708 LYS cc_start: 0.7136 (mtmt) cc_final: 0.6781 (mmtt) REVERT: D 226 TYR cc_start: 0.5346 (m-10) cc_final: 0.5137 (m-80) REVERT: D 251 ASN cc_start: 0.6314 (m110) cc_final: 0.6042 (m-40) REVERT: D 335 LYS cc_start: 0.5490 (OUTLIER) cc_final: 0.5206 (tmtt) REVERT: D 447 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.6560 (tt0) REVERT: D 539 LYS cc_start: 0.6849 (tttp) cc_final: 0.6388 (mtpp) REVERT: D 562 ASP cc_start: 0.5507 (p0) cc_final: 0.5239 (p0) REVERT: D 623 PHE cc_start: 0.6551 (OUTLIER) cc_final: 0.6063 (p90) REVERT: D 634 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.7135 (ptt180) REVERT: D 673 VAL cc_start: 0.6609 (OUTLIER) cc_final: 0.6406 (t) REVERT: D 674 LYS cc_start: 0.7353 (tttp) cc_final: 0.6839 (tttm) REVERT: D 708 LYS cc_start: 0.7124 (mtmt) cc_final: 0.6868 (mptt) outliers start: 131 outliers final: 89 residues processed: 474 average time/residue: 0.6482 time to fit residues: 343.0873 Evaluate side-chains 465 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 357 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 598 LYS Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 598 LYS Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 320 GLN Chi-restraints excluded: chain D residue 335 LYS Chi-restraints excluded: chain D residue 342 ARG Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 592 GLU Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 634 ARG Chi-restraints excluded: chain D residue 637 VAL Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 700 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 104 optimal weight: 10.0000 chunk 147 optimal weight: 7.9990 chunk 227 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 162 optimal weight: 8.9990 chunk 123 optimal weight: 8.9990 chunk 148 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN A 324 GLN B 280 ASN D 280 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.189318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.170800 restraints weight = 177057.340| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 5.44 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 21372 Z= 0.168 Angle : 0.646 13.021 29068 Z= 0.333 Chirality : 0.044 0.159 3051 Planarity : 0.006 0.054 3825 Dihedral : 9.695 81.174 3004 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 6.12 % Allowed : 23.00 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.23 (0.15), residues: 2630 helix: 0.61 (0.14), residues: 1129 sheet: 1.37 (0.57), residues: 48 loop : -0.81 (0.16), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 560 TYR 0.019 0.002 TYR D 226 PHE 0.016 0.002 PHE B 163 TRP 0.017 0.002 TRP A 189 HIS 0.009 0.002 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00374 (21368) covalent geometry : angle 0.64612 (29068) hydrogen bonds : bond 0.05622 ( 911) hydrogen bonds : angle 4.44360 ( 2316) Misc. bond : bond 0.02087 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 363 time to evaluate : 0.773 Fit side-chains REVERT: A 75 LYS cc_start: 0.7132 (OUTLIER) cc_final: 0.6653 (mttp) REVERT: A 144 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6838 (tpp-160) REVERT: A 335 LYS cc_start: 0.5183 (OUTLIER) cc_final: 0.4876 (tmtt) REVERT: A 342 ARG cc_start: 0.5424 (OUTLIER) cc_final: 0.5153 (ptp-110) REVERT: A 414 ARG cc_start: 0.6809 (ptt180) cc_final: 0.6428 (ptt180) REVERT: A 429 LYS cc_start: 0.6999 (OUTLIER) cc_final: 0.6591 (ttmm) REVERT: A 708 LYS cc_start: 0.7270 (mtmt) cc_final: 0.6731 (mmtt) REVERT: B 93 TRP cc_start: 0.6458 (m-90) cc_final: 0.6035 (m-90) REVERT: B 144 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6931 (tpp-160) REVERT: B 156 LYS cc_start: 0.7230 (mtmm) cc_final: 0.6729 (mtmt) REVERT: B 299 SER cc_start: 0.5456 (OUTLIER) cc_final: 0.5180 (t) REVERT: B 452 ASP cc_start: 0.6640 (m-30) cc_final: 0.5976 (t70) REVERT: B 575 ILE cc_start: 0.6580 (OUTLIER) cc_final: 0.6006 (mm) REVERT: B 581 ASN cc_start: 0.7131 (t0) cc_final: 0.6812 (t0) REVERT: B 623 PHE cc_start: 0.6553 (OUTLIER) cc_final: 0.6252 (p90) REVERT: B 667 ASP cc_start: 0.4778 (OUTLIER) cc_final: 0.4538 (t70) REVERT: B 674 LYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6726 (tttm) REVERT: C 64 LYS cc_start: 0.6382 (ttmm) cc_final: 0.6118 (ttpp) REVERT: C 75 LYS cc_start: 0.7194 (OUTLIER) cc_final: 0.6671 (mttp) REVERT: C 93 TRP cc_start: 0.6324 (m-90) cc_final: 0.6057 (m-90) REVERT: C 156 LYS cc_start: 0.7319 (mtmm) cc_final: 0.6793 (mtmt) REVERT: C 163 PHE cc_start: 0.7609 (m-80) cc_final: 0.7405 (m-80) REVERT: C 299 SER cc_start: 0.5858 (OUTLIER) cc_final: 0.5626 (t) REVERT: C 359 ILE cc_start: 0.6049 (OUTLIER) cc_final: 0.5659 (mp) REVERT: C 562 ASP cc_start: 0.5403 (p0) cc_final: 0.5176 (p0) REVERT: C 575 ILE cc_start: 0.6606 (OUTLIER) cc_final: 0.6090 (mm) REVERT: C 581 ASN cc_start: 0.7033 (t0) cc_final: 0.6762 (t0) REVERT: C 708 LYS cc_start: 0.7252 (mtmt) cc_final: 0.6809 (mmtt) REVERT: D 226 TYR cc_start: 0.5505 (m-10) cc_final: 0.5246 (m-80) REVERT: D 251 ASN cc_start: 0.6252 (m110) cc_final: 0.6030 (m-40) REVERT: D 335 LYS cc_start: 0.5334 (OUTLIER) cc_final: 0.5057 (tmtt) REVERT: D 447 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6590 (tt0) REVERT: D 479 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.6504 (mtp180) REVERT: D 539 LYS cc_start: 0.6574 (tttp) cc_final: 0.6135 (mtpp) REVERT: D 562 ASP cc_start: 0.5649 (p0) cc_final: 0.5394 (p0) REVERT: D 565 ASP cc_start: 0.6105 (t70) cc_final: 0.5726 (t0) REVERT: D 623 PHE cc_start: 0.6534 (OUTLIER) cc_final: 0.5962 (p90) REVERT: D 634 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.7032 (ptt180) REVERT: D 673 VAL cc_start: 0.6758 (OUTLIER) cc_final: 0.6522 (t) REVERT: D 674 LYS cc_start: 0.7406 (tttp) cc_final: 0.6899 (tttm) REVERT: D 708 LYS cc_start: 0.7243 (mtmt) cc_final: 0.6779 (mmtt) outliers start: 131 outliers final: 90 residues processed: 469 average time/residue: 0.6464 time to fit residues: 339.5004 Evaluate side-chains 471 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 360 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 429 LYS Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 580 ARG Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 598 LYS Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain B residue 634 ARG Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain B residue 674 LYS Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 598 LYS Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 320 GLN Chi-restraints excluded: chain D residue 335 LYS Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 592 GLU Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 634 ARG Chi-restraints excluded: chain D residue 637 VAL Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 659 SER Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 700 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 16 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 243 optimal weight: 0.8980 chunk 35 optimal weight: 0.0030 chunk 45 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 200 optimal weight: 9.9990 chunk 141 optimal weight: 0.0980 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.192432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.174195 restraints weight = 181402.636| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 5.46 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 21372 Z= 0.109 Angle : 0.550 10.518 29068 Z= 0.281 Chirality : 0.041 0.156 3051 Planarity : 0.005 0.054 3825 Dihedral : 8.897 70.813 3004 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 5.05 % Allowed : 23.94 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.25 (0.16), residues: 2630 helix: 1.07 (0.15), residues: 1132 sheet: 0.67 (0.59), residues: 58 loop : -0.57 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 381 TYR 0.018 0.001 TYR D 226 PHE 0.013 0.001 PHE B 163 TRP 0.017 0.002 TRP A 189 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00235 (21368) covalent geometry : angle 0.55001 (29068) hydrogen bonds : bond 0.04077 ( 911) hydrogen bonds : angle 4.20203 ( 2316) Misc. bond : bond 0.06169 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 378 time to evaluate : 0.835 Fit side-chains REVERT: A 64 LYS cc_start: 0.5964 (ttmm) cc_final: 0.5666 (ttpp) REVERT: A 75 LYS cc_start: 0.7053 (OUTLIER) cc_final: 0.6707 (mttp) REVERT: A 144 ARG cc_start: 0.7086 (OUTLIER) cc_final: 0.6786 (tpp-160) REVERT: A 342 ARG cc_start: 0.5390 (OUTLIER) cc_final: 0.5169 (ptp-110) REVERT: A 378 LEU cc_start: 0.6436 (OUTLIER) cc_final: 0.6180 (mt) REVERT: A 414 ARG cc_start: 0.6794 (ptt180) cc_final: 0.6405 (ptt180) REVERT: A 429 LYS cc_start: 0.7126 (OUTLIER) cc_final: 0.6708 (ttmm) REVERT: A 580 ARG cc_start: 0.7519 (ptt180) cc_final: 0.7154 (ptm160) REVERT: A 598 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.6756 (tmtp) REVERT: A 627 LYS cc_start: 0.7545 (mtpt) cc_final: 0.7139 (mtpp) REVERT: A 708 LYS cc_start: 0.7035 (mtmt) cc_final: 0.6618 (mmtt) REVERT: B 93 TRP cc_start: 0.6421 (m-90) cc_final: 0.6104 (m-90) REVERT: B 141 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.6956 (mtmm) REVERT: B 156 LYS cc_start: 0.7105 (mtmm) cc_final: 0.6642 (mtmt) REVERT: B 299 SER cc_start: 0.5553 (OUTLIER) cc_final: 0.5274 (t) REVERT: B 317 VAL cc_start: 0.6960 (t) cc_final: 0.6458 (p) REVERT: B 448 GLN cc_start: 0.7221 (OUTLIER) cc_final: 0.6980 (tp40) REVERT: B 452 ASP cc_start: 0.6549 (m-30) cc_final: 0.6001 (t70) REVERT: B 567 GLU cc_start: 0.5113 (tp30) cc_final: 0.4702 (mp0) REVERT: B 575 ILE cc_start: 0.6585 (OUTLIER) cc_final: 0.6025 (mm) REVERT: B 580 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7206 (ptm160) REVERT: B 581 ASN cc_start: 0.6837 (t0) cc_final: 0.6576 (t0) REVERT: B 592 GLU cc_start: 0.6107 (OUTLIER) cc_final: 0.5775 (mp0) REVERT: B 598 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.6797 (tmtp) REVERT: B 622 ASN cc_start: 0.7085 (m-40) cc_final: 0.6860 (m-40) REVERT: B 674 LYS cc_start: 0.7361 (OUTLIER) cc_final: 0.6995 (tttm) REVERT: C 42 ARG cc_start: 0.6069 (mmm-85) cc_final: 0.5567 (mmt90) REVERT: C 64 LYS cc_start: 0.6249 (ttmm) cc_final: 0.5932 (ttpp) REVERT: C 75 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6730 (mttp) REVERT: C 93 TRP cc_start: 0.6248 (m-90) cc_final: 0.6003 (m-90) REVERT: C 156 LYS cc_start: 0.7402 (mtmm) cc_final: 0.6872 (mtmt) REVERT: C 227 VAL cc_start: 0.5126 (m) cc_final: 0.4666 (t) REVERT: C 299 SER cc_start: 0.5869 (OUTLIER) cc_final: 0.5612 (t) REVERT: C 388 LYS cc_start: 0.4886 (mttt) cc_final: 0.4595 (mtmm) REVERT: C 519 GLU cc_start: 0.6565 (mm-30) cc_final: 0.6219 (mm-30) REVERT: C 562 ASP cc_start: 0.5401 (p0) cc_final: 0.5168 (p0) REVERT: C 581 ASN cc_start: 0.6976 (t0) cc_final: 0.6596 (t0) REVERT: C 592 GLU cc_start: 0.5994 (OUTLIER) cc_final: 0.5522 (mp0) REVERT: C 598 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.6896 (tmtp) REVERT: C 622 ASN cc_start: 0.7411 (m-40) cc_final: 0.7145 (m-40) REVERT: C 627 LYS cc_start: 0.7419 (mtpt) cc_final: 0.7099 (mtpp) REVERT: C 708 LYS cc_start: 0.7011 (mtmt) cc_final: 0.6703 (mmtt) REVERT: D 335 LYS cc_start: 0.5344 (OUTLIER) cc_final: 0.5042 (tmtt) REVERT: D 414 ARG cc_start: 0.7052 (ptt180) cc_final: 0.6725 (ptt180) REVERT: D 447 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6580 (tt0) REVERT: D 452 ASP cc_start: 0.6535 (m-30) cc_final: 0.6028 (t70) REVERT: D 539 LYS cc_start: 0.6681 (tttp) cc_final: 0.6264 (mtpp) REVERT: D 562 ASP cc_start: 0.5494 (p0) cc_final: 0.5260 (p0) REVERT: D 565 ASP cc_start: 0.6257 (t70) cc_final: 0.5909 (t0) REVERT: D 598 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.6816 (tmtp) REVERT: D 634 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6856 (ptt180) REVERT: D 673 VAL cc_start: 0.6675 (OUTLIER) cc_final: 0.6433 (t) REVERT: D 674 LYS cc_start: 0.7270 (tttp) cc_final: 0.6748 (tttm) REVERT: D 708 LYS cc_start: 0.7160 (mtmt) cc_final: 0.6709 (mmtt) outliers start: 108 outliers final: 45 residues processed: 466 average time/residue: 0.6536 time to fit residues: 341.3023 Evaluate side-chains 431 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 363 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 429 LYS Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 580 ARG Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 598 LYS Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 674 LYS Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 598 LYS Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 335 LYS Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 592 GLU Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 634 ARG Chi-restraints excluded: chain D residue 659 SER Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 700 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 120 optimal weight: 0.4980 chunk 110 optimal weight: 1.9990 chunk 214 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 chunk 230 optimal weight: 0.8980 chunk 252 optimal weight: 7.9990 chunk 182 optimal weight: 5.9990 chunk 42 optimal weight: 0.4980 chunk 166 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 249 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 ASN B 601 GLN C 601 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.194329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.176543 restraints weight = 178111.424| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 5.43 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.085 21372 Z= 0.102 Angle : 0.536 9.546 29068 Z= 0.272 Chirality : 0.040 0.156 3051 Planarity : 0.005 0.067 3825 Dihedral : 7.812 68.730 2963 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.60 % Allowed : 25.85 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.52 (0.16), residues: 2630 helix: 1.29 (0.15), residues: 1141 sheet: 0.65 (0.60), residues: 58 loop : -0.42 (0.17), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 583 TYR 0.015 0.001 TYR D 226 PHE 0.019 0.001 PHE B 455 TRP 0.016 0.001 TRP A 189 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00220 (21368) covalent geometry : angle 0.53567 (29068) hydrogen bonds : bond 0.03702 ( 911) hydrogen bonds : angle 4.09484 ( 2316) Misc. bond : bond 0.07114 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 381 time to evaluate : 0.766 Fit side-chains REVERT: A 64 LYS cc_start: 0.6176 (ttmm) cc_final: 0.5959 (ttpp) REVERT: A 378 LEU cc_start: 0.6402 (OUTLIER) cc_final: 0.6162 (mt) REVERT: A 414 ARG cc_start: 0.6860 (ptt180) cc_final: 0.6505 (ptt180) REVERT: A 598 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.6635 (tmtp) REVERT: A 624 ASP cc_start: 0.5186 (p0) cc_final: 0.4821 (p0) REVERT: A 627 LYS cc_start: 0.7401 (mtpt) cc_final: 0.7077 (mtpp) REVERT: A 708 LYS cc_start: 0.7095 (mtmt) cc_final: 0.6666 (mmtt) REVERT: B 64 LYS cc_start: 0.6242 (mtpm) cc_final: 0.6015 (ttmm) REVERT: B 93 TRP cc_start: 0.6388 (m-90) cc_final: 0.6103 (m-90) REVERT: B 141 LYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6955 (mtmm) REVERT: B 156 LYS cc_start: 0.7084 (mtmm) cc_final: 0.6592 (mtmt) REVERT: B 299 SER cc_start: 0.5440 (OUTLIER) cc_final: 0.5153 (t) REVERT: B 317 VAL cc_start: 0.6915 (t) cc_final: 0.6514 (p) REVERT: B 387 GLU cc_start: 0.5922 (tt0) cc_final: 0.5414 (tp30) REVERT: B 398 GLN cc_start: 0.6082 (mm110) cc_final: 0.5875 (mt0) REVERT: B 414 ARG cc_start: 0.6798 (ptt180) cc_final: 0.6447 (ptt180) REVERT: B 415 ASP cc_start: 0.6984 (p0) cc_final: 0.6617 (p0) REVERT: B 452 ASP cc_start: 0.6478 (m-30) cc_final: 0.6024 (t70) REVERT: B 567 GLU cc_start: 0.5219 (tp30) cc_final: 0.4880 (mp0) REVERT: B 580 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7289 (ptm160) REVERT: B 581 ASN cc_start: 0.7021 (t0) cc_final: 0.6719 (t0) REVERT: B 598 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.6763 (tmtp) REVERT: C 42 ARG cc_start: 0.6038 (mmm-85) cc_final: 0.5557 (mmt90) REVERT: C 64 LYS cc_start: 0.6218 (ttmm) cc_final: 0.5872 (mtpp) REVERT: C 75 LYS cc_start: 0.7290 (OUTLIER) cc_final: 0.6915 (mttp) REVERT: C 93 TRP cc_start: 0.6407 (m-90) cc_final: 0.6116 (m-90) REVERT: C 112 ARG cc_start: 0.6182 (mpp-170) cc_final: 0.5842 (mtt90) REVERT: C 156 LYS cc_start: 0.7342 (mtmm) cc_final: 0.6897 (mtmt) REVERT: C 227 VAL cc_start: 0.5152 (m) cc_final: 0.4624 (t) REVERT: C 299 SER cc_start: 0.5887 (OUTLIER) cc_final: 0.5601 (t) REVERT: C 519 GLU cc_start: 0.6438 (mm-30) cc_final: 0.6041 (mm-30) REVERT: C 562 ASP cc_start: 0.5477 (p0) cc_final: 0.5226 (p0) REVERT: C 598 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.6587 (tmtp) REVERT: C 627 LYS cc_start: 0.7395 (mtpt) cc_final: 0.7079 (mtpp) REVERT: C 708 LYS cc_start: 0.7129 (mtmt) cc_final: 0.6648 (mmtt) REVERT: D 335 LYS cc_start: 0.5357 (OUTLIER) cc_final: 0.5052 (tmtt) REVERT: D 414 ARG cc_start: 0.6864 (ptt180) cc_final: 0.6590 (ptt180) REVERT: D 447 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6394 (tt0) REVERT: D 452 ASP cc_start: 0.6528 (m-30) cc_final: 0.5924 (t70) REVERT: D 539 LYS cc_start: 0.6714 (tttp) cc_final: 0.6220 (mtpp) REVERT: D 560 ARG cc_start: 0.7893 (mtm-85) cc_final: 0.7652 (mtm-85) REVERT: D 562 ASP cc_start: 0.5684 (p0) cc_final: 0.5382 (p0) REVERT: D 598 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.6462 (tmtp) REVERT: D 673 VAL cc_start: 0.6619 (OUTLIER) cc_final: 0.6409 (t) REVERT: D 708 LYS cc_start: 0.7044 (mtmt) cc_final: 0.6635 (mmtt) outliers start: 77 outliers final: 42 residues processed: 444 average time/residue: 0.6050 time to fit residues: 302.8185 Evaluate side-chains 415 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 360 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 580 ARG Chi-restraints excluded: chain B residue 598 LYS Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 598 LYS Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 335 LYS Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 592 GLU Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 673 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 171 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 124 optimal weight: 0.5980 chunk 8 optimal weight: 20.0000 chunk 138 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 112 optimal weight: 30.0000 chunk 190 optimal weight: 6.9990 chunk 87 optimal weight: 0.5980 chunk 170 optimal weight: 9.9990 chunk 218 optimal weight: 50.0000 overall best weight: 5.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN A 601 GLN B 280 ASN C 581 ASN D 280 ASN D 601 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.188768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.170251 restraints weight = 178445.349| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 5.53 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 21372 Z= 0.194 Angle : 0.684 12.309 29068 Z= 0.354 Chirality : 0.046 0.190 3051 Planarity : 0.006 0.062 3825 Dihedral : 8.255 71.393 2941 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.09 % Allowed : 26.74 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.02 (0.16), residues: 2630 helix: 0.80 (0.14), residues: 1129 sheet: 0.74 (0.59), residues: 58 loop : -0.63 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 185 TYR 0.016 0.003 TYR B 582 PHE 0.015 0.002 PHE A 675 TRP 0.021 0.003 TRP A 93 HIS 0.007 0.002 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00432 (21368) covalent geometry : angle 0.68399 (29068) hydrogen bonds : bond 0.06061 ( 911) hydrogen bonds : angle 4.39131 ( 2316) Misc. bond : bond 0.02078 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 370 time to evaluate : 0.678 Fit side-chains REVERT: A 64 LYS cc_start: 0.6230 (ttmm) cc_final: 0.6025 (ttpp) REVERT: A 75 LYS cc_start: 0.7142 (OUTLIER) cc_final: 0.6784 (mtpp) REVERT: A 141 LYS cc_start: 0.7488 (mttp) cc_final: 0.7137 (mtmm) REVERT: A 144 ARG cc_start: 0.6967 (OUTLIER) cc_final: 0.6656 (tpp-160) REVERT: A 317 VAL cc_start: 0.6830 (OUTLIER) cc_final: 0.6427 (p) REVERT: A 335 LYS cc_start: 0.5258 (OUTLIER) cc_final: 0.4939 (tmtt) REVERT: A 414 ARG cc_start: 0.6844 (ptt180) cc_final: 0.6497 (ptt180) REVERT: A 567 GLU cc_start: 0.5316 (tp30) cc_final: 0.4728 (mp0) REVERT: A 627 LYS cc_start: 0.7579 (mtpt) cc_final: 0.7206 (mtpp) REVERT: A 708 LYS cc_start: 0.7288 (mtmt) cc_final: 0.6818 (mmtt) REVERT: B 93 TRP cc_start: 0.6503 (m-90) cc_final: 0.6067 (m-90) REVERT: B 156 LYS cc_start: 0.7236 (mtmm) cc_final: 0.6775 (mtmt) REVERT: B 256 ASP cc_start: 0.5866 (m-30) cc_final: 0.5519 (m-30) REVERT: B 299 SER cc_start: 0.5756 (OUTLIER) cc_final: 0.5443 (t) REVERT: B 317 VAL cc_start: 0.6901 (t) cc_final: 0.6565 (p) REVERT: B 452 ASP cc_start: 0.6606 (m-30) cc_final: 0.5918 (t0) REVERT: B 674 LYS cc_start: 0.6939 (tttt) cc_final: 0.6737 (tttp) REVERT: C 64 LYS cc_start: 0.6298 (ttmm) cc_final: 0.5993 (ttpp) REVERT: C 75 LYS cc_start: 0.7240 (OUTLIER) cc_final: 0.6749 (mttp) REVERT: C 77 ASP cc_start: 0.6213 (m-30) cc_final: 0.5905 (m-30) REVERT: C 156 LYS cc_start: 0.7376 (mtmm) cc_final: 0.6844 (mtmt) REVERT: C 299 SER cc_start: 0.5769 (OUTLIER) cc_final: 0.5514 (t) REVERT: C 562 ASP cc_start: 0.5455 (p0) cc_final: 0.5197 (p0) REVERT: C 708 LYS cc_start: 0.7211 (mtmt) cc_final: 0.6744 (mmtt) REVERT: D 226 TYR cc_start: 0.5560 (m-10) cc_final: 0.5277 (m-80) REVERT: D 335 LYS cc_start: 0.5456 (OUTLIER) cc_final: 0.5153 (tmtt) REVERT: D 447 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6681 (tt0) REVERT: D 539 LYS cc_start: 0.6732 (tttp) cc_final: 0.6361 (mtpp) REVERT: D 673 VAL cc_start: 0.6577 (OUTLIER) cc_final: 0.6347 (t) REVERT: D 674 LYS cc_start: 0.7013 (tttp) cc_final: 0.6761 (tttm) REVERT: D 708 LYS cc_start: 0.7220 (mtmt) cc_final: 0.6763 (mmtt) outliers start: 66 outliers final: 46 residues processed: 424 average time/residue: 0.6195 time to fit residues: 295.9283 Evaluate side-chains 423 residues out of total 2139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 367 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 519 GLU Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 623 PHE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 598 LYS Chi-restraints excluded: chain B residue 623 PHE Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 598 LYS Chi-restraints excluded: chain C residue 623 PHE Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain D residue 44 ASP Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 335 LYS Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 447 GLU Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain D residue 592 GLU Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 659 SER Chi-restraints excluded: chain D residue 673 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 31 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 200 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 280 ASN B 581 ASN B 601 GLN C 280 ASN D 280 ASN D 601 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.188199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.169739 restraints weight = 179997.655| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 5.45 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 21372 Z= 0.224 Angle : 0.743 14.284 29068 Z= 0.384 Chirality : 0.048 0.261 3051 Planarity : 0.007 0.059 3825 Dihedral : 8.641 76.216 2941 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.37 % Allowed : 26.74 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.33 (0.15), residues: 2630 helix: 0.45 (0.14), residues: 1129 sheet: 1.29 (0.58), residues: 48 loop : -0.79 (0.16), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 560 TYR 0.016 0.003 TYR B 582 PHE 0.024 0.003 PHE A 386 TRP 0.024 0.003 TRP A 93 HIS 0.009 0.002 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00508 (21368) covalent geometry : angle 0.74331 (29068) hydrogen bonds : bond 0.06529 ( 911) hydrogen bonds : angle 4.57329 ( 2316) Misc. bond : bond 0.04491 ( 4) =============================================================================== Job complete usr+sys time: 5998.66 seconds wall clock time: 102 minutes 48.82 seconds (6168.82 seconds total)