Starting phenix.real_space_refine on Wed Nov 19 08:58:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v11_21009/11_2025/6v11_21009.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v11_21009/11_2025/6v11_21009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v11_21009/11_2025/6v11_21009.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v11_21009/11_2025/6v11_21009.map" model { file = "/net/cci-nas-00/data/ceres_data/6v11_21009/11_2025/6v11_21009.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v11_21009/11_2025/6v11_21009.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 123 5.16 5 C 14250 2.51 5 N 3968 2.21 5 O 4275 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22626 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3798 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 467} Chain breaks: 3 Chain: "B" Number of atoms: 3829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3829 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 472} Chain breaks: 3 Chain: "C" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3883 Classifications: {'peptide': 503} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 478} Chain breaks: 4 Chain: "D" Number of atoms: 3594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3594 Classifications: {'peptide': 465} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 441} Chain breaks: 5 Chain: "E" Number of atoms: 3558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3558 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 441} Chain breaks: 5 Chain: "F" Number of atoms: 3829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3829 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 24, 'TRANS': 471} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.89, per 1000 atoms: 0.26 Number of scatterers: 22626 At special positions: 0 Unit cell: (133.4, 120.75, 155.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 123 16.00 P 10 15.00 O 4275 8.00 N 3968 7.00 C 14250 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 1.1 seconds 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5404 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 26 sheets defined 45.2% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 254 through 258 removed outlier: 3.816A pdb=" N ILE A 258 " --> pdb=" O LYS A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 289 through 301 removed outlier: 3.765A pdb=" N MET A 298 " --> pdb=" O TYR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 321 Processing helix chain 'A' and resid 327 through 344 Processing helix chain 'A' and resid 366 through 374 removed outlier: 3.736A pdb=" N LYS A 371 " --> pdb=" O GLN A 367 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 414 Processing helix chain 'A' and resid 440 through 444 Processing helix chain 'A' and resid 480 through 483 removed outlier: 3.663A pdb=" N ASP A 483 " --> pdb=" O PRO A 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 480 through 483' Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 506 through 512 Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 541 through 562 Processing helix chain 'A' and resid 574 through 579 removed outlier: 3.758A pdb=" N PHE A 578 " --> pdb=" O ASN A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 647 Processing helix chain 'A' and resid 657 through 661 Processing helix chain 'A' and resid 680 through 694 Processing helix chain 'A' and resid 718 through 729 removed outlier: 3.591A pdb=" N ALA A 725 " --> pdb=" O GLU A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 747 removed outlier: 5.211A pdb=" N ARG A 742 " --> pdb=" O ASP A 739 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 747 " --> pdb=" O LEU A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 755 removed outlier: 3.609A pdb=" N LEU A 755 " --> pdb=" O ILE A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 767 Processing helix chain 'B' and resid 254 through 259 removed outlier: 4.076A pdb=" N ILE B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 280 removed outlier: 3.813A pdb=" N LYS B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 301 removed outlier: 3.657A pdb=" N MET B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN B 300 " --> pdb=" O ASP B 296 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 301 " --> pdb=" O TRP B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 321 removed outlier: 3.635A pdb=" N ALA B 316 " --> pdb=" O ASP B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 344 removed outlier: 3.718A pdb=" N ASP B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG B 333 " --> pdb=" O ARG B 329 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR B 337 " --> pdb=" O ARG B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 374 removed outlier: 3.760A pdb=" N ALA B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS B 371 " --> pdb=" O GLN B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 414 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.896A pdb=" N LEU B 441 " --> pdb=" O SER B 438 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU B 442 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 453 No H-bonds generated for 'chain 'B' and resid 453 through 453' Processing helix chain 'B' and resid 455 through 458 Processing helix chain 'B' and resid 480 through 483 removed outlier: 3.588A pdb=" N ASP B 483 " --> pdb=" O PRO B 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 480 through 483' Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'B' and resid 524 through 535 removed outlier: 3.573A pdb=" N ILE B 528 " --> pdb=" O ASP B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 561 Processing helix chain 'B' and resid 631 through 648 Processing helix chain 'B' and resid 649 through 653 Processing helix chain 'B' and resid 657 through 661 removed outlier: 3.529A pdb=" N LYS B 661 " --> pdb=" O ASP B 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 657 through 661' Processing helix chain 'B' and resid 681 through 694 Processing helix chain 'B' and resid 718 through 729 removed outlier: 3.568A pdb=" N LYS B 722 " --> pdb=" O GLY B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 741 No H-bonds generated for 'chain 'B' and resid 739 through 741' Processing helix chain 'B' and resid 751 through 755 removed outlier: 3.728A pdb=" N ASP B 754 " --> pdb=" O VAL B 751 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B 755 " --> pdb=" O ILE B 752 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 751 through 755' Processing helix chain 'B' and resid 762 through 768 removed outlier: 3.737A pdb=" N VAL B 766 " --> pdb=" O ARG B 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 257 removed outlier: 4.384A pdb=" N ARG C 256 " --> pdb=" O ALA C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 279 Processing helix chain 'C' and resid 285 through 296 Processing helix chain 'C' and resid 297 through 299 No H-bonds generated for 'chain 'C' and resid 297 through 299' Processing helix chain 'C' and resid 313 through 321 Processing helix chain 'C' and resid 328 through 344 Processing helix chain 'C' and resid 363 through 374 removed outlier: 3.724A pdb=" N GLN C 367 " --> pdb=" O THR C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 414 Processing helix chain 'C' and resid 437 through 441 Processing helix chain 'C' and resid 478 through 483 removed outlier: 3.849A pdb=" N ASP C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 506 Processing helix chain 'C' and resid 524 through 532 Processing helix chain 'C' and resid 541 through 561 Processing helix chain 'C' and resid 574 through 579 removed outlier: 3.757A pdb=" N PHE C 578 " --> pdb=" O ASN C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 648 removed outlier: 3.838A pdb=" N MET C 634 " --> pdb=" O LEU C 630 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN C 635 " --> pdb=" O GLY C 631 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLU C 636 " --> pdb=" O GLU C 632 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER C 637 " --> pdb=" O VAL C 633 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG C 648 " --> pdb=" O VAL C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 661 Processing helix chain 'C' and resid 681 through 694 Processing helix chain 'C' and resid 718 through 729 removed outlier: 3.938A pdb=" N LYS C 722 " --> pdb=" O GLY C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 739 No H-bonds generated for 'chain 'C' and resid 737 through 739' Processing helix chain 'C' and resid 740 through 745 removed outlier: 3.733A pdb=" N GLU C 745 " --> pdb=" O LYS C 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 260 removed outlier: 3.762A pdb=" N ILE D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 279 Processing helix chain 'D' and resid 285 through 301 removed outlier: 4.519A pdb=" N MET D 298 " --> pdb=" O TYR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 321 removed outlier: 3.904A pdb=" N ASP D 321 " --> pdb=" O GLN D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 344 Processing helix chain 'D' and resid 364 through 374 Processing helix chain 'D' and resid 405 through 414 Processing helix chain 'D' and resid 440 through 445 Processing helix chain 'D' and resid 446 through 450 removed outlier: 3.662A pdb=" N ASN D 449 " --> pdb=" O PRO D 446 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL D 450 " --> pdb=" O GLU D 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 446 through 450' Processing helix chain 'D' and resid 478 through 483 Processing helix chain 'D' and resid 494 through 505 Processing helix chain 'D' and resid 506 through 512 Processing helix chain 'D' and resid 524 through 534 removed outlier: 3.773A pdb=" N ILE D 528 " --> pdb=" O ASP D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 558 Processing helix chain 'D' and resid 632 through 648 Processing helix chain 'D' and resid 657 through 661 Processing helix chain 'D' and resid 680 through 694 removed outlier: 3.750A pdb=" N MET D 684 " --> pdb=" O ALA D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 729 removed outlier: 3.872A pdb=" N LYS D 722 " --> pdb=" O GLY D 718 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA D 725 " --> pdb=" O GLU D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 745 removed outlier: 4.455A pdb=" N ARG D 742 " --> pdb=" O ASP D 739 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU D 745 " --> pdb=" O ARG D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 755 removed outlier: 3.892A pdb=" N ILE D 752 " --> pdb=" O PRO D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 763 through 768 Processing helix chain 'E' and resid 254 through 261 removed outlier: 3.962A pdb=" N ILE E 258 " --> pdb=" O LEU E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 279 removed outlier: 4.213A pdb=" N GLU E 269 " --> pdb=" O LYS E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 300 removed outlier: 4.040A pdb=" N VAL E 290 " --> pdb=" O ALA E 286 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG E 292 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE E 295 " --> pdb=" O VAL E 291 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N MET E 298 " --> pdb=" O TYR E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 344 Processing helix chain 'E' and resid 364 through 374 removed outlier: 4.033A pdb=" N SER E 368 " --> pdb=" O SER E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 414 removed outlier: 3.956A pdb=" N GLY E 414 " --> pdb=" O MET E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 445 removed outlier: 3.656A pdb=" N ASP E 445 " --> pdb=" O LEU E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 484 removed outlier: 3.871A pdb=" N ARG E 484 " --> pdb=" O PRO E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 505 removed outlier: 4.863A pdb=" N ASN E 500 " --> pdb=" O ASP E 496 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 512 Processing helix chain 'E' and resid 524 through 535 removed outlier: 3.569A pdb=" N ILE E 528 " --> pdb=" O ASP E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 561 Processing helix chain 'E' and resid 631 through 647 Processing helix chain 'E' and resid 657 through 662 Processing helix chain 'E' and resid 680 through 694 Processing helix chain 'E' and resid 718 through 728 removed outlier: 3.669A pdb=" N LYS E 722 " --> pdb=" O GLY E 718 " (cutoff:3.500A) Processing helix chain 'E' and resid 741 through 745 removed outlier: 3.865A pdb=" N LEU E 744 " --> pdb=" O LYS E 741 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU E 745 " --> pdb=" O ARG E 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 741 through 745' Processing helix chain 'E' and resid 748 through 755 removed outlier: 4.153A pdb=" N ILE E 752 " --> pdb=" O PRO E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 762 through 770 Processing helix chain 'F' and resid 254 through 260 removed outlier: 4.208A pdb=" N ILE F 258 " --> pdb=" O LEU F 254 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA F 260 " --> pdb=" O ARG F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 280 Processing helix chain 'F' and resid 285 through 301 removed outlier: 3.829A pdb=" N MET F 298 " --> pdb=" O TYR F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 321 Processing helix chain 'F' and resid 327 through 344 Processing helix chain 'F' and resid 362 through 374 removed outlier: 3.665A pdb=" N SER F 368 " --> pdb=" O SER F 364 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA F 370 " --> pdb=" O GLY F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 414 Processing helix chain 'F' and resid 440 through 445 Processing helix chain 'F' and resid 478 through 484 removed outlier: 3.887A pdb=" N ASP F 483 " --> pdb=" O ALA F 479 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG F 484 " --> pdb=" O PRO F 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 506 removed outlier: 3.635A pdb=" N LEU F 506 " --> pdb=" O ALA F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 506 through 512 Processing helix chain 'F' and resid 524 through 536 removed outlier: 3.722A pdb=" N ILE F 528 " --> pdb=" O ASP F 524 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N THR F 536 " --> pdb=" O ILE F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 561 Processing helix chain 'F' and resid 575 through 580 Processing helix chain 'F' and resid 634 through 647 Processing helix chain 'F' and resid 657 through 661 Processing helix chain 'F' and resid 681 through 694 removed outlier: 3.818A pdb=" N CYS F 685 " --> pdb=" O GLY F 681 " (cutoff:3.500A) Processing helix chain 'F' and resid 718 through 729 removed outlier: 3.551A pdb=" N LYS F 722 " --> pdb=" O GLY F 718 " (cutoff:3.500A) Processing helix chain 'F' and resid 740 through 745 removed outlier: 3.870A pdb=" N GLU F 745 " --> pdb=" O LYS F 741 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 753 removed outlier: 3.733A pdb=" N ILE F 752 " --> pdb=" O PRO F 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 762 through 770 removed outlier: 3.577A pdb=" N VAL F 766 " --> pdb=" O ARG F 762 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE F 769 " --> pdb=" O ASP F 765 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 377 through 381 removed outlier: 7.101A pdb=" N VAL A 378 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ASP A 423 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N MET A 380 " --> pdb=" O ASP A 423 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N PHE A 420 " --> pdb=" O VAL A 469 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N THR A 471 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU A 422 " --> pdb=" O THR A 471 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU A 352 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE A 351 " --> pdb=" O GLU A 486 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ILE A 488 " --> pdb=" O ILE A 351 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N CYS A 353 " --> pdb=" O ILE A 488 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 521 through 523 Processing sheet with id=AA3, first strand: chain 'A' and resid 597 through 598 removed outlier: 6.758A pdb=" N THR A 625 " --> pdb=" O VAL A 666 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 601 through 602 Processing sheet with id=AA5, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.901A pdb=" N ALA A 702 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL A 734 " --> pdb=" O HIS A 758 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL A 760 " --> pdb=" O VAL A 734 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE A 736 " --> pdb=" O VAL A 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 706 through 707 removed outlier: 4.058A pdb=" N GLU A 706 " --> pdb=" O LEU A 714 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 378 through 381 removed outlier: 6.806A pdb=" N VAL B 378 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ASP B 423 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N MET B 380 " --> pdb=" O ASP B 423 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL B 469 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU B 352 " --> pdb=" O ALA B 470 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N SER B 472 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU B 354 " --> pdb=" O SER B 472 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE B 351 " --> pdb=" O GLU B 486 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE B 488 " --> pdb=" O ILE B 351 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N CYS B 353 " --> pdb=" O ILE B 488 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 522 through 523 removed outlier: 7.006A pdb=" N THR B 522 " --> pdb=" O ILE B 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 624 through 627 removed outlier: 6.363A pdb=" N THR B 625 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA B 702 " --> pdb=" O LEU B 735 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL B 734 " --> pdb=" O HIS B 758 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL B 760 " --> pdb=" O VAL B 734 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE B 736 " --> pdb=" O VAL B 760 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 706 through 707 removed outlier: 3.885A pdb=" N GLU B 706 " --> pdb=" O LEU B 714 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 376 through 378 removed outlier: 6.441A pdb=" N GLN C 376 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU C 421 " --> pdb=" O GLN C 376 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL C 378 " --> pdb=" O LEU C 421 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ASP C 423 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL C 469 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU C 352 " --> pdb=" O ALA C 470 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N SER C 472 " --> pdb=" O LEU C 352 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU C 354 " --> pdb=" O SER C 472 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE C 351 " --> pdb=" O GLU C 486 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE C 488 " --> pdb=" O ILE C 351 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N CYS C 353 " --> pdb=" O ILE C 488 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 521 through 523 removed outlier: 6.409A pdb=" N THR C 522 " --> pdb=" O ILE C 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 624 through 628 removed outlier: 6.212A pdb=" N THR C 625 " --> pdb=" O VAL C 666 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL C 668 " --> pdb=" O THR C 625 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR C 627 " --> pdb=" O VAL C 668 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N VAL C 701 " --> pdb=" O GLN C 597 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR C 599 " --> pdb=" O VAL C 701 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 419 through 422 removed outlier: 6.497A pdb=" N LEU D 352 " --> pdb=" O ALA D 470 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N SER D 472 " --> pdb=" O LEU D 352 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU D 354 " --> pdb=" O SER D 472 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE D 351 " --> pdb=" O GLU D 486 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 521 through 522 Processing sheet with id=AB7, first strand: chain 'D' and resid 598 through 602 removed outlier: 3.884A pdb=" N ASP D 609 " --> pdb=" O ALA D 602 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR D 627 " --> pdb=" O VAL D 666 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 701 through 703 removed outlier: 6.428A pdb=" N ALA D 702 " --> pdb=" O LEU D 735 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 706 through 707 removed outlier: 4.084A pdb=" N GLU D 706 " --> pdb=" O LEU D 714 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 378 through 380 removed outlier: 6.187A pdb=" N VAL E 378 " --> pdb=" O LEU E 421 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N PHE E 420 " --> pdb=" O VAL E 469 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N THR E 471 " --> pdb=" O PHE E 420 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU E 422 " --> pdb=" O THR E 471 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU E 352 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 521 through 523 Processing sheet with id=AC3, first strand: chain 'E' and resid 597 through 602 removed outlier: 3.544A pdb=" N ILE E 613 " --> pdb=" O VAL E 598 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA E 602 " --> pdb=" O ASP E 609 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP E 609 " --> pdb=" O ALA E 602 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 701 through 703 removed outlier: 6.631A pdb=" N VAL E 734 " --> pdb=" O HIS E 758 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL E 760 " --> pdb=" O VAL E 734 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ILE E 736 " --> pdb=" O VAL E 760 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 377 through 380 removed outlier: 5.819A pdb=" N PHE F 420 " --> pdb=" O VAL F 469 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N THR F 471 " --> pdb=" O PHE F 420 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU F 422 " --> pdb=" O THR F 471 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU F 352 " --> pdb=" O ALA F 470 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N SER F 472 " --> pdb=" O LEU F 352 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU F 354 " --> pdb=" O SER F 472 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE F 351 " --> pdb=" O GLU F 486 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE F 488 " --> pdb=" O ILE F 351 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N CYS F 353 " --> pdb=" O ILE F 488 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 521 through 523 Processing sheet with id=AC7, first strand: chain 'F' and resid 624 through 627 removed outlier: 6.645A pdb=" N THR F 625 " --> pdb=" O VAL F 666 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS F 665 " --> pdb=" O ALA F 616 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL F 701 " --> pdb=" O GLN F 597 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR F 599 " --> pdb=" O VAL F 701 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL F 734 " --> pdb=" O HIS F 758 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL F 760 " --> pdb=" O VAL F 734 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE F 736 " --> pdb=" O VAL F 760 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 706 through 707 removed outlier: 3.654A pdb=" N GLU F 706 " --> pdb=" O LEU F 714 " (cutoff:3.500A) 875 hydrogen bonds defined for protein. 2559 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: 4.07 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5497 1.33 - 1.45: 3621 1.45 - 1.57: 13586 1.57 - 1.69: 15 1.69 - 1.81: 216 Bond restraints: 22935 Sorted by residual: bond pdb=" CA ILE C 638 " pdb=" C ILE C 638 " ideal model delta sigma weight residual 1.523 1.470 0.053 1.27e-02 6.20e+03 1.77e+01 bond pdb=" CA MET C 634 " pdb=" C MET C 634 " ideal model delta sigma weight residual 1.522 1.473 0.049 1.36e-02 5.41e+03 1.31e+01 bond pdb=" CA ILE C 638 " pdb=" CB ILE C 638 " ideal model delta sigma weight residual 1.540 1.498 0.042 1.25e-02 6.40e+03 1.13e+01 bond pdb=" N MET C 634 " pdb=" CA MET C 634 " ideal model delta sigma weight residual 1.459 1.419 0.040 1.25e-02 6.40e+03 1.03e+01 bond pdb=" N ALA C 640 " pdb=" CA ALA C 640 " ideal model delta sigma weight residual 1.459 1.425 0.034 1.21e-02 6.83e+03 7.83e+00 ... (remaining 22930 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 29350 2.15 - 4.30: 1331 4.30 - 6.45: 223 6.45 - 8.60: 49 8.60 - 10.76: 6 Bond angle restraints: 30959 Sorted by residual: angle pdb=" N GLU C 632 " pdb=" CA GLU C 632 " pdb=" C GLU C 632 " ideal model delta sigma weight residual 111.07 119.22 -8.15 1.07e+00 8.73e-01 5.80e+01 angle pdb=" O VAL C 633 " pdb=" C VAL C 633 " pdb=" N MET C 634 " ideal model delta sigma weight residual 121.87 127.45 -5.58 1.01e+00 9.80e-01 3.05e+01 angle pdb=" CA VAL C 633 " pdb=" C VAL C 633 " pdb=" N MET C 634 " ideal model delta sigma weight residual 117.53 111.25 6.28 1.19e+00 7.06e-01 2.78e+01 angle pdb=" N SER C 629 " pdb=" CA SER C 629 " pdb=" C SER C 629 " ideal model delta sigma weight residual 110.53 117.39 -6.86 1.32e+00 5.74e-01 2.70e+01 angle pdb=" C ALA C 640 " pdb=" N ALA C 641 " pdb=" CA ALA C 641 " ideal model delta sigma weight residual 120.28 113.32 6.96 1.34e+00 5.57e-01 2.70e+01 ... (remaining 30954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.19: 13815 23.19 - 46.38: 436 46.38 - 69.57: 24 69.57 - 92.76: 6 92.76 - 115.94: 1 Dihedral angle restraints: 14282 sinusoidal: 5925 harmonic: 8357 Sorted by residual: dihedral pdb=" O1B ADP A 800 " pdb=" O3A ADP A 800 " pdb=" PB ADP A 800 " pdb=" PA ADP A 800 " ideal model delta sinusoidal sigma weight residual -60.00 55.94 -115.94 1 2.00e+01 2.50e-03 3.45e+01 dihedral pdb=" CA LYS A 517 " pdb=" C LYS A 517 " pdb=" N LYS A 518 " pdb=" CA LYS A 518 " ideal model delta harmonic sigma weight residual 180.00 152.65 27.35 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA PRO A 678 " pdb=" C PRO A 678 " pdb=" N SER A 679 " pdb=" CA SER A 679 " ideal model delta harmonic sigma weight residual 180.00 152.95 27.05 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 14279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2842 0.075 - 0.149: 728 0.149 - 0.224: 56 0.224 - 0.299: 4 0.299 - 0.373: 1 Chirality restraints: 3631 Sorted by residual: chirality pdb=" CA MET C 634 " pdb=" N MET C 634 " pdb=" C MET C 634 " pdb=" CB MET C 634 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CG LEU B 365 " pdb=" CB LEU B 365 " pdb=" CD1 LEU B 365 " pdb=" CD2 LEU B 365 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CB VAL B 606 " pdb=" CA VAL B 606 " pdb=" CG1 VAL B 606 " pdb=" CG2 VAL B 606 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.26 2.00e-01 2.50e+01 1.76e+00 ... (remaining 3628 not shown) Planarity restraints: 3938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 507 " 0.048 5.00e-02 4.00e+02 7.15e-02 8.19e+00 pdb=" N PRO B 508 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 508 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 508 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 507 " 0.044 5.00e-02 4.00e+02 6.67e-02 7.11e+00 pdb=" N PRO D 508 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO D 508 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 508 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 507 " -0.043 5.00e-02 4.00e+02 6.46e-02 6.67e+00 pdb=" N PRO E 508 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO E 508 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 508 " -0.036 5.00e-02 4.00e+02 ... (remaining 3935 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4819 2.77 - 3.31: 20659 3.31 - 3.84: 35947 3.84 - 4.37: 40969 4.37 - 4.90: 69075 Nonbonded interactions: 171469 Sorted by model distance: nonbonded pdb=" OG1 THR B 536 " pdb=" OE1 GLU B 538 " model vdw 2.243 3.040 nonbonded pdb=" OD1 ASP E 423 " pdb=" OG1 THR E 471 " model vdw 2.253 3.040 nonbonded pdb=" O ALA E 267 " pdb=" OG1 THR E 271 " model vdw 2.260 3.040 nonbonded pdb=" OG1 THR F 363 " pdb=" O3B ADP F 800 " model vdw 2.262 3.040 nonbonded pdb=" O VAL B 595 " pdb=" OG SER B 690 " model vdw 2.267 3.040 ... (remaining 171464 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 253 through 300 or resid 316 through 380 or resid 404 thro \ ugh 426 or resid 437 through 448 or resid 464 through 532 or resid 534 through 5 \ 60 or resid 566 through 579 or resid 597 through 674 or resid 678 through 685 or \ (resid 686 and (name N or name CA or name C or name O )) or resid 687 through 7 \ 75)) selection = (chain 'B' and (resid 253 through 280 or resid 288 through 300 or resid 316 thro \ ugh 380 or resid 404 through 426 or resid 437 through 448 or resid 464 through 5 \ 32 or resid 534 through 560 or resid 566 through 579 or resid 597 through 674 or \ resid 678 through 685 or (resid 686 and (name N or name CA or name C or name O \ )) or resid 687 through 775)) selection = (chain 'C' and (resid 253 through 280 or resid 288 through 300 or resid 316 thro \ ugh 380 or resid 404 through 426 or resid 437 through 448 or resid 464 through 5 \ 60 or resid 566 through 579 or resid 597 through 674 or resid 678 through 685 or \ (resid 686 and (name N or name CA or name C or name O )) or resid 687 through 7 \ 75)) selection = (chain 'D' and (resid 253 through 280 or resid 288 through 300 or resid 316 thro \ ugh 380 or resid 404 through 448 or resid 464 through 532 or resid 534 through 6 \ 74 or resid 678 through 685 or (resid 686 and (name N or name CA or name C or na \ me O )) or resid 687 through 775)) selection = (chain 'E' and (resid 253 through 280 or resid 288 through 380 or resid 404 thro \ ugh 426 or resid 437 through 532 or resid 534 through 560 or resid 566 through 5 \ 79 or resid 597 through 674 or resid 678 through 685 or (resid 686 and (name N o \ r name CA or name C or name O )) or resid 687 through 775)) selection = (chain 'F' and (resid 253 through 280 or resid 288 through 300 or resid 316 thro \ ugh 380 or resid 404 through 426 or resid 437 through 448 or resid 464 through 5 \ 32 or resid 534 through 560 or resid 566 through 579 or resid 597 through 775)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 21.850 Find NCS groups from input model: 0.570 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: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 22935 Z= 0.370 Angle : 1.074 10.755 30959 Z= 0.576 Chirality : 0.062 0.373 3631 Planarity : 0.008 0.072 3938 Dihedral : 11.183 115.944 8878 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.90 % Allowed : 4.97 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.51 (0.12), residues: 2857 helix: -3.49 (0.09), residues: 1209 sheet: -1.97 (0.24), residues: 403 loop : -2.67 (0.15), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG C 553 TYR 0.026 0.003 TYR A 535 PHE 0.020 0.003 PHE B 658 TRP 0.033 0.003 TRP C 603 HIS 0.012 0.002 HIS E 727 Details of bonding type rmsd covalent geometry : bond 0.00840 (22935) covalent geometry : angle 1.07381 (30959) hydrogen bonds : bond 0.19122 ( 875) hydrogen bonds : angle 9.96498 ( 2559) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 636 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.7422 (tmm) cc_final: 0.6911 (tmm) REVERT: A 296 ASP cc_start: 0.8700 (m-30) cc_final: 0.8307 (m-30) REVERT: A 351 ILE cc_start: 0.7629 (mp) cc_final: 0.6931 (mm) REVERT: A 606 VAL cc_start: 0.7459 (m) cc_final: 0.7216 (t) REVERT: B 262 LYS cc_start: 0.8391 (ttpt) cc_final: 0.7829 (tptt) REVERT: B 296 ASP cc_start: 0.8633 (m-30) cc_final: 0.8304 (m-30) REVERT: B 522 THR cc_start: 0.8969 (p) cc_final: 0.8713 (t) REVERT: C 268 ARG cc_start: 0.8433 (mtm110) cc_final: 0.7793 (ttm-80) REVERT: C 297 TRP cc_start: 0.8739 (m100) cc_final: 0.7533 (m100) REVERT: C 426 ASP cc_start: 0.7655 (t0) cc_final: 0.7441 (t0) REVERT: C 529 MET cc_start: 0.8254 (mmm) cc_final: 0.8015 (tpt) REVERT: D 270 LYS cc_start: 0.8880 (mmpt) cc_final: 0.8619 (pttt) REVERT: D 294 TYR cc_start: 0.7375 (t80) cc_final: 0.6097 (m-10) REVERT: D 336 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7094 (mt-10) REVERT: D 728 ARG cc_start: 0.7423 (ttp-110) cc_final: 0.7088 (ttp80) REVERT: E 280 MET cc_start: 0.6455 (mtt) cc_final: 0.5675 (mmm) REVERT: E 333 ARG cc_start: 0.8186 (tpt170) cc_final: 0.7791 (ttt180) REVERT: E 354 LEU cc_start: 0.8684 (mt) cc_final: 0.8387 (mp) REVERT: E 516 ILE cc_start: 0.8186 (mt) cc_final: 0.7934 (mm) REVERT: E 609 ASP cc_start: 0.9217 (p0) cc_final: 0.8869 (p0) REVERT: E 633 VAL cc_start: 0.7706 (t) cc_final: 0.7074 (p) REVERT: F 380 MET cc_start: 0.7959 (tpt) cc_final: 0.7530 (tpp) REVERT: F 456 TYR cc_start: 0.6963 (t80) cc_final: 0.6617 (m-80) outliers start: 22 outliers final: 8 residues processed: 651 average time/residue: 0.1853 time to fit residues: 177.8080 Evaluate side-chains 351 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 343 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 629 SER Chi-restraints excluded: chain C residue 634 MET Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain F residue 668 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 0.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 ASN B 758 HIS ** C 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 ASN C 476 ASN C 758 HIS D 276 GLN D 476 ASN E 571 ASN E 635 GLN F 448 GLN F 597 GLN F 773 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.114820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.091213 restraints weight = 52482.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.093695 restraints weight = 28762.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.095327 restraints weight = 19066.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.096407 restraints weight = 14213.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.097105 restraints weight = 11638.066| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 22935 Z= 0.205 Angle : 0.765 9.289 30959 Z= 0.386 Chirality : 0.048 0.215 3631 Planarity : 0.006 0.067 3938 Dihedral : 7.818 112.370 3187 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.06 % Allowed : 12.43 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.14), residues: 2857 helix: -1.74 (0.13), residues: 1247 sheet: -1.49 (0.25), residues: 383 loop : -2.17 (0.16), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 484 TYR 0.027 0.002 TYR E 325 PHE 0.012 0.001 PHE E 420 TRP 0.021 0.002 TRP D 603 HIS 0.005 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00467 (22935) covalent geometry : angle 0.76463 (30959) hydrogen bonds : bond 0.04771 ( 875) hydrogen bonds : angle 6.06307 ( 2559) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 368 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 262 LYS cc_start: 0.8351 (ttpt) cc_final: 0.7970 (tptt) REVERT: B 296 ASP cc_start: 0.8460 (m-30) cc_final: 0.8238 (m-30) REVERT: B 321 ASP cc_start: 0.8157 (m-30) cc_final: 0.7542 (t0) REVERT: B 522 THR cc_start: 0.8792 (p) cc_final: 0.8500 (t) REVERT: C 529 MET cc_start: 0.8442 (mmm) cc_final: 0.8104 (tpt) REVERT: D 336 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7624 (mp0) REVERT: D 552 CYS cc_start: 0.5417 (OUTLIER) cc_final: 0.5142 (p) REVERT: D 728 ARG cc_start: 0.7501 (ttp-110) cc_final: 0.7198 (ttp80) REVERT: E 280 MET cc_start: 0.6378 (mtt) cc_final: 0.5677 (ptt) REVERT: E 294 TYR cc_start: 0.5134 (m-80) cc_final: 0.4924 (m-80) REVERT: E 333 ARG cc_start: 0.8350 (tpt170) cc_final: 0.7593 (ttt180) REVERT: E 354 LEU cc_start: 0.8742 (mt) cc_final: 0.8515 (mp) REVERT: E 529 MET cc_start: 0.8482 (tpt) cc_final: 0.8112 (tmm) REVERT: E 609 ASP cc_start: 0.9415 (p0) cc_final: 0.9118 (p0) REVERT: E 633 VAL cc_start: 0.7869 (t) cc_final: 0.7564 (p) REVERT: F 271 THR cc_start: 0.9012 (m) cc_final: 0.8696 (t) REVERT: F 456 TYR cc_start: 0.7105 (t80) cc_final: 0.6781 (m-80) outliers start: 75 outliers final: 46 residues processed: 427 average time/residue: 0.1615 time to fit residues: 106.9701 Evaluate side-chains 349 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 302 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 518 LYS Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 650 ASP Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 764 ASP Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 552 CYS Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 634 MET Chi-restraints excluded: chain D residue 758 HIS Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 426 ASP Chi-restraints excluded: chain E residue 552 CYS Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 685 CYS Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 300 GLN Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 497 GLU Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain F residue 512 GLU Chi-restraints excluded: chain F residue 579 LEU Chi-restraints excluded: chain F residue 618 VAL Chi-restraints excluded: chain F residue 668 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 169 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 chunk 281 optimal weight: 7.9990 chunk 150 optimal weight: 4.9990 chunk 162 optimal weight: 9.9990 chunk 206 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 171 optimal weight: 20.0000 chunk 277 optimal weight: 0.9980 chunk 284 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 HIS A 408 GLN C 448 GLN C 473 ASN C 476 ASN C 514 ASN D 476 ASN E 597 GLN E 635 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.111791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.088066 restraints weight = 52949.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.090496 restraints weight = 29371.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.092086 restraints weight = 19399.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.093170 restraints weight = 14531.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.093878 restraints weight = 11902.131| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 22935 Z= 0.240 Angle : 0.759 9.762 30959 Z= 0.376 Chirality : 0.048 0.189 3631 Planarity : 0.005 0.051 3938 Dihedral : 7.584 112.964 3182 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.28 % Allowed : 13.94 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.15), residues: 2857 helix: -1.04 (0.14), residues: 1230 sheet: -1.37 (0.25), residues: 392 loop : -1.93 (0.17), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 537 TYR 0.022 0.002 TYR D 294 PHE 0.018 0.002 PHE A 452 TRP 0.025 0.002 TRP D 603 HIS 0.007 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00550 (22935) covalent geometry : angle 0.75856 (30959) hydrogen bonds : bond 0.04519 ( 875) hydrogen bonds : angle 5.64577 ( 2559) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 305 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.7040 (tmm) cc_final: 0.6827 (tmm) REVERT: A 296 ASP cc_start: 0.8834 (m-30) cc_final: 0.8451 (m-30) REVERT: A 582 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8149 (mp10) REVERT: B 262 LYS cc_start: 0.8420 (ttpt) cc_final: 0.7983 (tptt) REVERT: B 265 LYS cc_start: 0.8983 (mmmt) cc_final: 0.8524 (mmmt) REVERT: B 296 ASP cc_start: 0.8485 (m-30) cc_final: 0.8197 (m-30) REVERT: B 321 ASP cc_start: 0.8230 (m-30) cc_final: 0.7869 (t0) REVERT: C 263 MET cc_start: 0.8160 (mmm) cc_final: 0.7665 (mmm) REVERT: C 476 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.8034 (t0) REVERT: C 529 MET cc_start: 0.8471 (mmm) cc_final: 0.8133 (tpt) REVERT: C 634 MET cc_start: 0.8111 (mmt) cc_final: 0.7728 (mmt) REVERT: D 270 LYS cc_start: 0.8982 (mmpt) cc_final: 0.8597 (pttt) REVERT: D 336 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7625 (mp0) REVERT: D 634 MET cc_start: 0.8318 (mmp) cc_final: 0.8083 (mmp) REVERT: D 728 ARG cc_start: 0.7739 (ttp-110) cc_final: 0.7261 (ttp80) REVERT: E 280 MET cc_start: 0.6282 (mtt) cc_final: 0.5583 (ptt) REVERT: E 333 ARG cc_start: 0.8322 (tpt170) cc_final: 0.7576 (ttt180) REVERT: E 354 LEU cc_start: 0.8740 (mt) cc_final: 0.8489 (mp) REVERT: E 529 MET cc_start: 0.8359 (tpt) cc_final: 0.7982 (tmm) REVERT: E 635 GLN cc_start: 0.8509 (mt0) cc_final: 0.7982 (tm-30) REVERT: F 263 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.7195 (ttt) outliers start: 105 outliers final: 69 residues processed: 381 average time/residue: 0.1513 time to fit residues: 91.2082 Evaluate side-chains 329 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 257 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 552 CYS Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 710 ARG Chi-restraints excluded: chain C residue 281 MET Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 476 ASN Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 605 GLU Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 650 ASP Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 764 ASP Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 682 ILE Chi-restraints excluded: chain D residue 758 HIS Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 426 ASP Chi-restraints excluded: chain E residue 548 ILE Chi-restraints excluded: chain E residue 552 CYS Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 685 CYS Chi-restraints excluded: chain E residue 723 LEU Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 579 LEU Chi-restraints excluded: chain F residue 618 VAL Chi-restraints excluded: chain F residue 668 VAL Chi-restraints excluded: chain F residue 682 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 142 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 199 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 191 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 272 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 149 optimal weight: 6.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 500 ASN D 476 ASN D 514 ASN F 510 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.114125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.090503 restraints weight = 52503.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.093029 restraints weight = 28769.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.094689 restraints weight = 18894.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.095768 restraints weight = 14076.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.096446 restraints weight = 11522.665| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22935 Z= 0.122 Angle : 0.649 11.974 30959 Z= 0.318 Chirality : 0.045 0.265 3631 Planarity : 0.005 0.046 3938 Dihedral : 7.122 110.353 3182 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.63 % Allowed : 15.04 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.15), residues: 2857 helix: -0.49 (0.15), residues: 1236 sheet: -1.12 (0.26), residues: 387 loop : -1.73 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 537 TYR 0.018 0.001 TYR F 294 PHE 0.017 0.001 PHE A 452 TRP 0.021 0.001 TRP D 303 HIS 0.003 0.001 HIS B 758 Details of bonding type rmsd covalent geometry : bond 0.00276 (22935) covalent geometry : angle 0.64902 (30959) hydrogen bonds : bond 0.03673 ( 875) hydrogen bonds : angle 5.12272 ( 2559) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 325 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ARG cc_start: 0.8198 (mmt90) cc_final: 0.7941 (mmt90) REVERT: A 296 ASP cc_start: 0.8739 (m-30) cc_final: 0.8416 (m-30) REVERT: A 467 MET cc_start: 0.7167 (ttm) cc_final: 0.6625 (mtp) REVERT: A 582 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.7735 (mp10) REVERT: B 262 LYS cc_start: 0.8409 (ttpt) cc_final: 0.8042 (tptt) REVERT: B 321 ASP cc_start: 0.8068 (m-30) cc_final: 0.7748 (t0) REVERT: B 336 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6820 (mt-10) REVERT: B 485 MET cc_start: 0.8192 (mtp) cc_final: 0.7744 (ttm) REVERT: B 522 THR cc_start: 0.8816 (p) cc_final: 0.8484 (t) REVERT: B 559 LEU cc_start: 0.9273 (mt) cc_final: 0.9053 (tt) REVERT: C 263 MET cc_start: 0.8276 (mmm) cc_final: 0.7792 (mmm) REVERT: C 476 ASN cc_start: 0.8539 (t0) cc_final: 0.8262 (t0) REVERT: C 529 MET cc_start: 0.8416 (mmm) cc_final: 0.8086 (tpt) REVERT: D 270 LYS cc_start: 0.8667 (mmpt) cc_final: 0.8322 (ptpt) REVERT: D 336 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7539 (mp0) REVERT: D 448 GLN cc_start: 0.6840 (tm-30) cc_final: 0.6468 (tm-30) REVERT: D 716 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.8741 (tp) REVERT: D 728 ARG cc_start: 0.7765 (ttp-110) cc_final: 0.7136 (ttp80) REVERT: E 280 MET cc_start: 0.6117 (mtt) cc_final: 0.5451 (ptt) REVERT: E 529 MET cc_start: 0.8455 (tpt) cc_final: 0.7922 (tmm) REVERT: E 635 GLN cc_start: 0.8296 (mt0) cc_final: 0.7849 (tm-30) REVERT: F 263 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.7127 (ttt) REVERT: F 448 GLN cc_start: 0.8685 (mp10) cc_final: 0.8222 (mp10) outliers start: 89 outliers final: 53 residues processed: 383 average time/residue: 0.1467 time to fit residues: 89.9944 Evaluate side-chains 333 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 277 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain C residue 281 MET Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 650 ASP Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 716 ILE Chi-restraints excluded: chain D residue 758 HIS Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 425 ILE Chi-restraints excluded: chain E residue 552 CYS Chi-restraints excluded: chain E residue 618 VAL Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 685 CYS Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 618 VAL Chi-restraints excluded: chain F residue 630 LEU Chi-restraints excluded: chain F residue 668 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 285 optimal weight: 3.9990 chunk 275 optimal weight: 7.9990 chunk 212 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 288 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 254 optimal weight: 6.9990 chunk 266 optimal weight: 0.8980 chunk 101 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 GLN C 510 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.121114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.095431 restraints weight = 57289.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.098441 restraints weight = 29234.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.100361 restraints weight = 18513.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.101589 restraints weight = 13547.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.102268 restraints weight = 10993.411| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22935 Z= 0.137 Angle : 0.655 13.406 30959 Z= 0.319 Chirality : 0.045 0.351 3631 Planarity : 0.004 0.046 3938 Dihedral : 6.926 109.801 3182 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.47 % Allowed : 16.59 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.16), residues: 2857 helix: -0.24 (0.15), residues: 1242 sheet: -0.96 (0.26), residues: 397 loop : -1.68 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 333 TYR 0.015 0.001 TYR F 294 PHE 0.017 0.001 PHE F 452 TRP 0.015 0.001 TRP D 603 HIS 0.004 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00317 (22935) covalent geometry : angle 0.65482 (30959) hydrogen bonds : bond 0.03570 ( 875) hydrogen bonds : angle 5.01014 ( 2559) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 302 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.6536 (tmm) cc_final: 0.6251 (tmm) REVERT: A 292 ARG cc_start: 0.8168 (mmt90) cc_final: 0.7909 (mmt90) REVERT: A 296 ASP cc_start: 0.8886 (m-30) cc_final: 0.8557 (m-30) REVERT: A 402 MET cc_start: 0.5170 (ppp) cc_final: 0.4714 (ppp) REVERT: A 467 MET cc_start: 0.7311 (ttm) cc_final: 0.6636 (mtp) REVERT: A 582 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8204 (mp10) REVERT: B 262 LYS cc_start: 0.8323 (ttpt) cc_final: 0.7925 (tptt) REVERT: B 321 ASP cc_start: 0.8212 (m-30) cc_final: 0.7828 (t0) REVERT: B 336 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6956 (mt-10) REVERT: B 522 THR cc_start: 0.8881 (p) cc_final: 0.8553 (t) REVERT: B 559 LEU cc_start: 0.9282 (mt) cc_final: 0.9053 (tt) REVERT: B 609 ASP cc_start: 0.8019 (t0) cc_final: 0.7727 (t0) REVERT: B 710 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7517 (ptm160) REVERT: C 529 MET cc_start: 0.8494 (mmm) cc_final: 0.8134 (tpt) REVERT: D 270 LYS cc_start: 0.8648 (mmpt) cc_final: 0.8209 (ptpt) REVERT: D 336 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7709 (mp0) REVERT: D 467 MET cc_start: 0.8218 (ttt) cc_final: 0.7910 (ttt) REVERT: D 482 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8669 (mt) REVERT: D 716 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8760 (tp) REVERT: D 728 ARG cc_start: 0.7843 (ttp-110) cc_final: 0.7134 (ttp80) REVERT: E 280 MET cc_start: 0.5863 (mtt) cc_final: 0.5518 (mmp) REVERT: E 529 MET cc_start: 0.8455 (tpt) cc_final: 0.7813 (tmm) REVERT: E 635 GLN cc_start: 0.8118 (mt0) cc_final: 0.7496 (tm-30) REVERT: E 703 MET cc_start: 0.7763 (ttm) cc_final: 0.7462 (ptm) REVERT: F 440 LEU cc_start: 0.8311 (pt) cc_final: 0.7950 (pt) REVERT: F 447 GLU cc_start: 0.8254 (pm20) cc_final: 0.7784 (pm20) REVERT: F 448 GLN cc_start: 0.8691 (mp10) cc_final: 0.8064 (mp10) outliers start: 85 outliers final: 62 residues processed: 362 average time/residue: 0.1526 time to fit residues: 87.9989 Evaluate side-chains 332 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 266 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 552 CYS Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 710 ARG Chi-restraints excluded: chain C residue 281 MET Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 650 ASP Chi-restraints excluded: chain C residue 675 LYS Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 764 ASP Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 634 MET Chi-restraints excluded: chain D residue 716 ILE Chi-restraints excluded: chain D residue 758 HIS Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 552 CYS Chi-restraints excluded: chain E residue 618 VAL Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 685 CYS Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 512 GLU Chi-restraints excluded: chain F residue 579 LEU Chi-restraints excluded: chain F residue 618 VAL Chi-restraints excluded: chain F residue 630 LEU Chi-restraints excluded: chain F residue 668 VAL Chi-restraints excluded: chain F residue 724 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 58 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 114 optimal weight: 0.0870 chunk 78 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 264 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 HIS C 476 ASN D 476 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.123449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.098854 restraints weight = 57933.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.101994 restraints weight = 31293.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.104286 restraints weight = 18004.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.104778 restraints weight = 13369.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.104733 restraints weight = 10961.967| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22935 Z= 0.108 Angle : 0.629 12.671 30959 Z= 0.306 Chirality : 0.044 0.344 3631 Planarity : 0.004 0.044 3938 Dihedral : 6.612 105.588 3182 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.89 % Allowed : 17.77 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.16), residues: 2857 helix: -0.00 (0.15), residues: 1259 sheet: -0.75 (0.25), residues: 411 loop : -1.61 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 379 TYR 0.024 0.001 TYR E 626 PHE 0.014 0.001 PHE F 452 TRP 0.014 0.001 TRP D 603 HIS 0.005 0.001 HIS B 773 Details of bonding type rmsd covalent geometry : bond 0.00242 (22935) covalent geometry : angle 0.62916 (30959) hydrogen bonds : bond 0.03159 ( 875) hydrogen bonds : angle 4.70951 ( 2559) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 323 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ARG cc_start: 0.8120 (mmt90) cc_final: 0.7851 (mmt90) REVERT: A 296 ASP cc_start: 0.8986 (m-30) cc_final: 0.8639 (m-30) REVERT: A 402 MET cc_start: 0.5220 (ppp) cc_final: 0.4773 (ppp) REVERT: A 467 MET cc_start: 0.7318 (ttm) cc_final: 0.6634 (mtp) REVERT: A 473 ASN cc_start: 0.8695 (m110) cc_final: 0.8455 (m-40) REVERT: A 582 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.7846 (mp10) REVERT: B 262 LYS cc_start: 0.8211 (ttpt) cc_final: 0.7826 (tptt) REVERT: B 321 ASP cc_start: 0.8124 (m-30) cc_final: 0.7770 (t0) REVERT: B 336 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6906 (mt-10) REVERT: B 379 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8325 (mtp85) REVERT: B 380 MET cc_start: 0.7811 (tpt) cc_final: 0.7507 (tpp) REVERT: B 522 THR cc_start: 0.8857 (p) cc_final: 0.8529 (t) REVERT: B 559 LEU cc_start: 0.9313 (mt) cc_final: 0.9071 (tt) REVERT: B 609 ASP cc_start: 0.7999 (t0) cc_final: 0.7651 (t0) REVERT: C 297 TRP cc_start: 0.8809 (m100) cc_final: 0.8606 (m100) REVERT: C 298 MET cc_start: 0.7894 (mmt) cc_final: 0.7632 (mmp) REVERT: C 529 MET cc_start: 0.8502 (mmm) cc_final: 0.8158 (tpt) REVERT: D 263 MET cc_start: 0.7417 (mmm) cc_final: 0.7201 (mmm) REVERT: D 298 MET cc_start: 0.7776 (mmt) cc_final: 0.7575 (mmp) REVERT: D 336 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7680 (mp0) REVERT: D 467 MET cc_start: 0.8184 (ttt) cc_final: 0.7909 (ttt) REVERT: D 716 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8715 (tp) REVERT: D 728 ARG cc_start: 0.7859 (ttp-110) cc_final: 0.7130 (ttp80) REVERT: E 280 MET cc_start: 0.5779 (mtt) cc_final: 0.5481 (mmp) REVERT: E 529 MET cc_start: 0.8437 (tpt) cc_final: 0.7730 (tmm) REVERT: E 635 GLN cc_start: 0.8050 (mt0) cc_final: 0.7737 (tm-30) REVERT: E 703 MET cc_start: 0.7651 (ttm) cc_final: 0.7422 (ptm) REVERT: F 298 MET cc_start: 0.8730 (tpp) cc_final: 0.8506 (tpp) REVERT: F 440 LEU cc_start: 0.8455 (pt) cc_final: 0.8170 (pt) REVERT: F 447 GLU cc_start: 0.8395 (pm20) cc_final: 0.8001 (pm20) REVERT: F 448 GLN cc_start: 0.8811 (mp10) cc_final: 0.8122 (mp10) outliers start: 71 outliers final: 50 residues processed: 372 average time/residue: 0.1508 time to fit residues: 89.4218 Evaluate side-chains 333 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 280 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 552 CYS Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 379 ARG Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 650 ASP Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 634 MET Chi-restraints excluded: chain D residue 716 ILE Chi-restraints excluded: chain D residue 758 HIS Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 552 CYS Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 663 ASP Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 685 CYS Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 579 LEU Chi-restraints excluded: chain F residue 630 LEU Chi-restraints excluded: chain F residue 668 VAL Chi-restraints excluded: chain F residue 724 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 219 optimal weight: 10.0000 chunk 243 optimal weight: 0.0670 chunk 264 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 257 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 HIS C 476 ASN D 476 ASN D 665 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.118012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.092196 restraints weight = 58040.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.095066 restraints weight = 30134.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.096909 restraints weight = 19392.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.098129 restraints weight = 14273.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.098894 restraints weight = 11592.466| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 22935 Z= 0.233 Angle : 0.732 9.012 30959 Z= 0.360 Chirality : 0.047 0.175 3631 Planarity : 0.005 0.044 3938 Dihedral : 6.931 105.814 3182 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.59 % Allowed : 18.47 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.16), residues: 2857 helix: -0.12 (0.15), residues: 1242 sheet: -0.69 (0.26), residues: 384 loop : -1.60 (0.17), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 329 TYR 0.015 0.002 TYR E 325 PHE 0.022 0.001 PHE A 452 TRP 0.012 0.001 TRP D 603 HIS 0.008 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00538 (22935) covalent geometry : angle 0.73226 (30959) hydrogen bonds : bond 0.03935 ( 875) hydrogen bonds : angle 5.13987 ( 2559) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 273 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.6484 (tmm) cc_final: 0.6243 (tmm) REVERT: A 296 ASP cc_start: 0.8818 (m-30) cc_final: 0.8423 (m-30) REVERT: A 402 MET cc_start: 0.5328 (ppp) cc_final: 0.4907 (ppp) REVERT: A 582 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8119 (mp10) REVERT: A 634 MET cc_start: 0.8801 (mmp) cc_final: 0.8539 (mmt) REVERT: B 262 LYS cc_start: 0.8278 (ttpt) cc_final: 0.7901 (tptt) REVERT: B 321 ASP cc_start: 0.8312 (m-30) cc_final: 0.7906 (t0) REVERT: B 336 GLU cc_start: 0.7334 (mt-10) cc_final: 0.7097 (mt-10) REVERT: B 410 MET cc_start: 0.8573 (tpp) cc_final: 0.8278 (tpp) REVERT: B 522 THR cc_start: 0.8984 (p) cc_final: 0.8683 (t) REVERT: B 525 ASP cc_start: 0.8291 (p0) cc_final: 0.7953 (p0) REVERT: B 559 LEU cc_start: 0.9350 (mt) cc_final: 0.9062 (tt) REVERT: B 634 MET cc_start: 0.8681 (tpp) cc_final: 0.8431 (tpt) REVERT: C 467 MET cc_start: 0.8661 (ttm) cc_final: 0.8198 (mtp) REVERT: C 476 ASN cc_start: 0.8741 (OUTLIER) cc_final: 0.8210 (t0) REVERT: C 529 MET cc_start: 0.8590 (mmm) cc_final: 0.8184 (tpt) REVERT: D 298 MET cc_start: 0.7677 (mmt) cc_final: 0.7383 (mmp) REVERT: D 336 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7796 (mp0) REVERT: D 467 MET cc_start: 0.8317 (ttt) cc_final: 0.8006 (ttt) REVERT: D 493 TYR cc_start: 0.7724 (m-80) cc_final: 0.7356 (m-80) REVERT: D 716 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8664 (tp) REVERT: D 728 ARG cc_start: 0.8101 (ttp-110) cc_final: 0.7333 (ttp80) REVERT: E 280 MET cc_start: 0.5705 (mtt) cc_final: 0.5400 (mmp) REVERT: E 528 ILE cc_start: 0.9189 (mm) cc_final: 0.8970 (tp) REVERT: E 529 MET cc_start: 0.8475 (tpt) cc_final: 0.7815 (tmm) REVERT: E 703 MET cc_start: 0.7859 (ttm) cc_final: 0.7597 (ptm) REVERT: F 298 MET cc_start: 0.8691 (tpp) cc_final: 0.8471 (tpp) REVERT: F 440 LEU cc_start: 0.8364 (pt) cc_final: 0.8030 (pt) REVERT: F 447 GLU cc_start: 0.8251 (pm20) cc_final: 0.8005 (pm20) REVERT: F 448 GLN cc_start: 0.8729 (mp10) cc_final: 0.8037 (mp10) outliers start: 88 outliers final: 64 residues processed: 336 average time/residue: 0.1433 time to fit residues: 78.3156 Evaluate side-chains 328 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 261 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 552 CYS Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 453 ASN Chi-restraints excluded: chain C residue 476 ASN Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 650 ASP Chi-restraints excluded: chain C residue 675 LYS Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 634 MET Chi-restraints excluded: chain D residue 716 ILE Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 758 HIS Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 552 CYS Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 663 ASP Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 685 CYS Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 512 GLU Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 579 LEU Chi-restraints excluded: chain F residue 618 VAL Chi-restraints excluded: chain F residue 630 LEU Chi-restraints excluded: chain F residue 668 VAL Chi-restraints excluded: chain F residue 682 ILE Chi-restraints excluded: chain F residue 724 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 169 optimal weight: 6.9990 chunk 274 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 145 optimal weight: 0.9990 chunk 151 optimal weight: 0.8980 chunk 213 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 72 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 476 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.120882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.094669 restraints weight = 56402.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.097679 restraints weight = 29113.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.099601 restraints weight = 18562.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.100856 restraints weight = 13671.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.101665 restraints weight = 11118.949| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22935 Z= 0.142 Angle : 0.665 11.747 30959 Z= 0.323 Chirality : 0.045 0.316 3631 Planarity : 0.004 0.043 3938 Dihedral : 6.707 105.101 3180 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.22 % Allowed : 19.08 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.16), residues: 2857 helix: 0.06 (0.15), residues: 1246 sheet: -0.59 (0.26), residues: 403 loop : -1.57 (0.18), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 588 TYR 0.035 0.001 TYR E 626 PHE 0.020 0.001 PHE F 452 TRP 0.012 0.001 TRP D 603 HIS 0.004 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00331 (22935) covalent geometry : angle 0.66466 (30959) hydrogen bonds : bond 0.03432 ( 875) hydrogen bonds : angle 4.86708 ( 2559) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 270 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.6664 (tmm) cc_final: 0.6403 (tmm) REVERT: A 296 ASP cc_start: 0.8917 (m-30) cc_final: 0.8573 (m-30) REVERT: A 402 MET cc_start: 0.5253 (ppp) cc_final: 0.4867 (ppp) REVERT: A 582 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8144 (mp10) REVERT: B 262 LYS cc_start: 0.8317 (ttpt) cc_final: 0.7878 (tptt) REVERT: B 321 ASP cc_start: 0.8261 (m-30) cc_final: 0.7943 (t0) REVERT: B 336 GLU cc_start: 0.7293 (mt-10) cc_final: 0.7054 (mt-10) REVERT: B 380 MET cc_start: 0.7833 (tpt) cc_final: 0.7227 (tpt) REVERT: B 522 THR cc_start: 0.8970 (p) cc_final: 0.8637 (t) REVERT: B 559 LEU cc_start: 0.9391 (mt) cc_final: 0.9086 (tt) REVERT: B 609 ASP cc_start: 0.8101 (t0) cc_final: 0.7786 (t0) REVERT: B 634 MET cc_start: 0.8637 (tpp) cc_final: 0.8417 (tpt) REVERT: C 467 MET cc_start: 0.8596 (ttm) cc_final: 0.8152 (mtp) REVERT: C 529 MET cc_start: 0.8544 (mmm) cc_final: 0.8174 (tpt) REVERT: D 298 MET cc_start: 0.7649 (mmt) cc_final: 0.7365 (mmp) REVERT: D 336 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7740 (mp0) REVERT: D 493 TYR cc_start: 0.7643 (m-80) cc_final: 0.7400 (m-80) REVERT: D 716 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8688 (tp) REVERT: E 280 MET cc_start: 0.5565 (mtt) cc_final: 0.5323 (mmp) REVERT: E 529 MET cc_start: 0.8465 (tpt) cc_final: 0.7807 (tmm) REVERT: E 703 MET cc_start: 0.7702 (ttm) cc_final: 0.7450 (ptm) REVERT: F 298 MET cc_start: 0.8742 (tpp) cc_final: 0.8487 (tpp) REVERT: F 440 LEU cc_start: 0.8456 (pt) cc_final: 0.8170 (pt) REVERT: F 447 GLU cc_start: 0.8334 (pm20) cc_final: 0.8062 (pm20) REVERT: F 448 GLN cc_start: 0.8763 (mp10) cc_final: 0.8092 (mp10) outliers start: 79 outliers final: 65 residues processed: 328 average time/residue: 0.1458 time to fit residues: 77.3402 Evaluate side-chains 326 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 259 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 552 CYS Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 650 ASP Chi-restraints excluded: chain C residue 675 LYS Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 634 MET Chi-restraints excluded: chain D residue 716 ILE Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 758 HIS Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 426 ASP Chi-restraints excluded: chain E residue 552 CYS Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 663 ASP Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 685 CYS Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 487 VAL Chi-restraints excluded: chain F residue 512 GLU Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 579 LEU Chi-restraints excluded: chain F residue 618 VAL Chi-restraints excluded: chain F residue 630 LEU Chi-restraints excluded: chain F residue 668 VAL Chi-restraints excluded: chain F residue 710 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 242 optimal weight: 0.8980 chunk 131 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 276 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 162 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 119 optimal weight: 0.0870 chunk 98 optimal weight: 9.9990 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.120699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.094966 restraints weight = 57556.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.097933 restraints weight = 29556.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.099844 restraints weight = 18786.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.101086 restraints weight = 13773.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.101887 restraints weight = 11160.175| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22935 Z= 0.131 Angle : 0.664 10.518 30959 Z= 0.323 Chirality : 0.045 0.302 3631 Planarity : 0.004 0.043 3938 Dihedral : 6.560 104.419 3180 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.10 % Allowed : 19.45 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.16), residues: 2857 helix: 0.16 (0.15), residues: 1240 sheet: -0.51 (0.26), residues: 396 loop : -1.47 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 292 TYR 0.040 0.001 TYR E 626 PHE 0.018 0.001 PHE F 452 TRP 0.013 0.001 TRP D 603 HIS 0.004 0.001 HIS E 667 Details of bonding type rmsd covalent geometry : bond 0.00306 (22935) covalent geometry : angle 0.66431 (30959) hydrogen bonds : bond 0.03290 ( 875) hydrogen bonds : angle 4.76639 ( 2559) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 278 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 ASP cc_start: 0.8855 (m-30) cc_final: 0.8461 (m-30) REVERT: A 402 MET cc_start: 0.5150 (ppp) cc_final: 0.4844 (ppp) REVERT: A 582 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8163 (mp10) REVERT: B 262 LYS cc_start: 0.8291 (ttpt) cc_final: 0.7878 (tptt) REVERT: B 321 ASP cc_start: 0.8246 (m-30) cc_final: 0.7938 (t0) REVERT: B 380 MET cc_start: 0.7830 (tpt) cc_final: 0.7218 (tpt) REVERT: B 457 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7884 (tm) REVERT: B 522 THR cc_start: 0.8955 (p) cc_final: 0.8636 (t) REVERT: B 525 ASP cc_start: 0.8368 (p0) cc_final: 0.8125 (p0) REVERT: B 559 LEU cc_start: 0.9381 (mt) cc_final: 0.9095 (tt) REVERT: B 609 ASP cc_start: 0.8089 (t0) cc_final: 0.7761 (t0) REVERT: C 467 MET cc_start: 0.8595 (ttm) cc_final: 0.8159 (mtp) REVERT: C 529 MET cc_start: 0.8558 (mmm) cc_final: 0.8184 (tpt) REVERT: C 570 ILE cc_start: 0.8841 (mt) cc_final: 0.8520 (tp) REVERT: D 263 MET cc_start: 0.7447 (mmm) cc_final: 0.7149 (mmm) REVERT: D 278 LEU cc_start: 0.6229 (mm) cc_final: 0.5929 (mm) REVERT: D 298 MET cc_start: 0.7633 (mmt) cc_final: 0.7349 (mmp) REVERT: D 336 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7751 (mp0) REVERT: D 493 TYR cc_start: 0.7626 (m-80) cc_final: 0.7419 (m-80) REVERT: D 634 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8184 (mmm) REVERT: D 716 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8667 (tp) REVERT: E 529 MET cc_start: 0.8520 (tpt) cc_final: 0.7853 (tmm) REVERT: E 636 GLU cc_start: 0.8063 (pp20) cc_final: 0.7787 (pp20) REVERT: F 440 LEU cc_start: 0.8407 (pt) cc_final: 0.8182 (pt) REVERT: F 448 GLN cc_start: 0.8760 (mp10) cc_final: 0.8349 (mp10) outliers start: 76 outliers final: 63 residues processed: 329 average time/residue: 0.1475 time to fit residues: 78.9413 Evaluate side-chains 331 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 264 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 552 CYS Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 453 ASN Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 650 ASP Chi-restraints excluded: chain C residue 675 LYS Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 634 MET Chi-restraints excluded: chain D residue 716 ILE Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain D residue 758 HIS Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 426 ASP Chi-restraints excluded: chain E residue 552 CYS Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 663 ASP Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 685 CYS Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 512 GLU Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 579 LEU Chi-restraints excluded: chain F residue 618 VAL Chi-restraints excluded: chain F residue 630 LEU Chi-restraints excluded: chain F residue 668 VAL Chi-restraints excluded: chain F residue 710 ARG Chi-restraints excluded: chain F residue 724 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 147 optimal weight: 1.9990 chunk 288 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 225 optimal weight: 0.6980 chunk 259 optimal weight: 2.9990 chunk 242 optimal weight: 8.9990 chunk 151 optimal weight: 0.0670 chunk 7 optimal weight: 2.9990 overall best weight: 1.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 476 ASN D 558 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 = 0.120897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.094842 restraints weight = 57222.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.097886 restraints weight = 28387.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.099847 restraints weight = 17798.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.101125 restraints weight = 12927.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.101947 restraints weight = 10408.698| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22935 Z= 0.137 Angle : 0.683 10.343 30959 Z= 0.330 Chirality : 0.045 0.318 3631 Planarity : 0.004 0.043 3938 Dihedral : 6.519 104.495 3180 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.85 % Allowed : 20.02 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.16), residues: 2857 helix: 0.22 (0.15), residues: 1238 sheet: -0.48 (0.26), residues: 400 loop : -1.42 (0.18), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 292 TYR 0.030 0.001 TYR E 626 PHE 0.015 0.001 PHE C 420 TRP 0.013 0.001 TRP D 603 HIS 0.004 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00321 (22935) covalent geometry : angle 0.68333 (30959) hydrogen bonds : bond 0.03260 ( 875) hydrogen bonds : angle 4.74224 ( 2559) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5714 Ramachandran restraints generated. 2857 Oldfield, 0 Emsley, 2857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 275 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.6578 (tmm) cc_final: 0.5983 (tmm) REVERT: A 296 ASP cc_start: 0.8870 (m-30) cc_final: 0.8479 (m-30) REVERT: A 402 MET cc_start: 0.5119 (ppp) cc_final: 0.4820 (ppp) REVERT: A 582 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8132 (mp10) REVERT: B 262 LYS cc_start: 0.8260 (ttpt) cc_final: 0.7863 (tptt) REVERT: B 321 ASP cc_start: 0.8286 (m-30) cc_final: 0.7953 (t0) REVERT: B 380 MET cc_start: 0.7844 (tpt) cc_final: 0.7279 (tpt) REVERT: B 457 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7910 (tm) REVERT: B 522 THR cc_start: 0.8968 (p) cc_final: 0.8700 (t) REVERT: B 525 ASP cc_start: 0.8419 (p0) cc_final: 0.8194 (p0) REVERT: B 559 LEU cc_start: 0.9381 (mt) cc_final: 0.9097 (tt) REVERT: B 609 ASP cc_start: 0.8112 (t0) cc_final: 0.7771 (t0) REVERT: C 265 LYS cc_start: 0.8387 (pptt) cc_final: 0.8095 (pptt) REVERT: C 458 GLU cc_start: 0.8521 (mp0) cc_final: 0.8310 (mp0) REVERT: C 467 MET cc_start: 0.8556 (ttm) cc_final: 0.8100 (mtp) REVERT: C 529 MET cc_start: 0.8593 (mmm) cc_final: 0.8203 (tpt) REVERT: C 570 ILE cc_start: 0.8865 (mt) cc_final: 0.8522 (tp) REVERT: D 263 MET cc_start: 0.7463 (mmm) cc_final: 0.7182 (mmm) REVERT: D 298 MET cc_start: 0.7588 (mmt) cc_final: 0.7316 (mmp) REVERT: D 336 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7776 (mp0) REVERT: D 447 GLU cc_start: 0.7751 (pm20) cc_final: 0.7538 (pm20) REVERT: D 482 LEU cc_start: 0.8936 (mt) cc_final: 0.8547 (mt) REVERT: D 634 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8230 (mmm) REVERT: D 716 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8668 (tp) REVERT: E 529 MET cc_start: 0.8500 (tpt) cc_final: 0.7920 (tmm) REVERT: E 703 MET cc_start: 0.7557 (ptm) cc_final: 0.7240 (tmm) REVERT: F 299 LEU cc_start: 0.8928 (mt) cc_final: 0.8724 (mt) REVERT: F 440 LEU cc_start: 0.8475 (pt) cc_final: 0.8273 (pt) REVERT: F 448 GLN cc_start: 0.8749 (mp10) cc_final: 0.8398 (mp10) REVERT: F 485 MET cc_start: 0.8839 (pmm) cc_final: 0.8468 (pmm) outliers start: 70 outliers final: 63 residues processed: 324 average time/residue: 0.1459 time to fit residues: 76.5255 Evaluate side-chains 328 residues out of total 2454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 261 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 552 CYS Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 710 ARG Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 453 ASN Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 650 ASP Chi-restraints excluded: chain C residue 675 LYS Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 558 ASN Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 634 MET Chi-restraints excluded: chain D residue 716 ILE Chi-restraints excluded: chain D residue 734 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain E residue 405 LYS Chi-restraints excluded: chain E residue 426 ASP Chi-restraints excluded: chain E residue 552 CYS Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 663 ASP Chi-restraints excluded: chain E residue 668 VAL Chi-restraints excluded: chain E residue 685 CYS Chi-restraints excluded: chain E residue 731 ILE Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain F residue 512 GLU Chi-restraints excluded: chain F residue 579 LEU Chi-restraints excluded: chain F residue 618 VAL Chi-restraints excluded: chain F residue 630 LEU Chi-restraints excluded: chain F residue 668 VAL Chi-restraints excluded: chain F residue 710 ARG Chi-restraints excluded: chain F residue 724 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 230 optimal weight: 0.6980 chunk 117 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 151 optimal weight: 0.9980 chunk 160 optimal weight: 9.9990 chunk 156 optimal weight: 0.9980 chunk 229 optimal weight: 0.0370 chunk 7 optimal weight: 3.9990 overall best weight: 1.3460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 HIS ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.121318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.095106 restraints weight = 57508.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.098218 restraints weight = 28680.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.100220 restraints weight = 17937.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.101509 restraints weight = 13009.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.102293 restraints weight = 10483.170| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22935 Z= 0.129 Angle : 0.680 12.614 30959 Z= 0.326 Chirality : 0.045 0.319 3631 Planarity : 0.004 0.043 3938 Dihedral : 6.444 104.269 3180 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.89 % Allowed : 20.30 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.16), residues: 2857 helix: 0.27 (0.15), residues: 1240 sheet: -0.38 (0.26), residues: 394 loop : -1.38 (0.18), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 292 TYR 0.028 0.001 TYR E 626 PHE 0.019 0.001 PHE F 452 TRP 0.014 0.001 TRP D 603 HIS 0.003 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00302 (22935) covalent geometry : angle 0.67970 (30959) hydrogen bonds : bond 0.03181 ( 875) hydrogen bonds : angle 4.66634 ( 2559) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3981.34 seconds wall clock time: 69 minutes 43.90 seconds (4183.90 seconds total)